「NAMD」の版間の差分

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(namd.confの編集)
(水の付加)
 
(同じ利用者による、間の10版が非表示)
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=== データベースからダウンロード ===
 
=== データベースからダウンロード ===
 
 データベース先:https://www.rcsb.org/pdb/home/home.do
 
 データベース先:https://www.rcsb.org/pdb/home/home.do
 +
 +
=== 水素の付加 ===
 +
  Chimera Tools -> Structture Edition -> AddHで実施
 +
 +
=== 水の排除 ===
 
   psfファイルを作成する際に、水を除いておく必要がある。
 
   psfファイルを作成する際に、水を除いておく必要がある。
 
 PDBファイルを詠み込んで、分子を選択した後,File -> Save  Coordinatresで保存
 
 PDBファイルを詠み込んで、分子を選択した後,File -> Save  Coordinatresで保存
行24: 行29:
 
  Extensions -> Modeling -> Automatic PSF Builder
 
  Extensions -> Modeling -> Automatic PSF Builder
 
==== Step-1: Input and Output Files ====
 
==== Step-1: Input and Output Files ====
   分子の選択:Molecule
+
   
  output basename: 出力ファイルのベースネーム(.pdb/.psfを除いたもの)
+
分子の選択をして下さい。
 +
  Molecule
 +
 
 +
出力用のベースネームを設定して下さい。
 +
  output basename:  
 +
 
 +
 出力ファイルのベースネーム(.pdb/.psfを除いたもの)
 +
 
 +
  ディレクトリがずれていると出力がうまくいかない事があるので、vmd consoleでcdで移動するか、もしくは、Output basenameにディレクトリ毎指定する必要がある)
 
  Topologyファイルの選択(通常はデフォールトでよい)
 
  Topologyファイルの選択(通常はデフォールトでよい)
 
  Load input filesを押す
 
  Load input filesを押す
==== Step-2: Selections to include in PSF/PDB
+
 
 +
==== Step-2: Selections to include in PSF/PDB ====
 +
 
 
   Everything(default) (ここで、たんぱく質(protein)と核酸(Nucleic acid)の選択も可能)
 
   Everything(default) (ここで、たんぱく質(protein)と核酸(Nucleic acid)の選択も可能)
 
   Guess and split chains using current selections を押す
 
   Guess and split chains using current selections を押す
行35: 行50:
 
  編集したい場合は、こちらで編集
 
  編集したい場合は、こちらで編集
 
 
 
 
 +
 
==== Step-3: ====
 
==== Step-3: ====
 
   チェーン(共有結合でつながっているもの)の編集が必要なら行う
 
   チェーン(共有結合でつながっているもの)の編集が必要なら行う
行42: 行58:
 
  Apply patches and finish PSF/PDB. を押す
 
  Apply patches and finish PSF/PDB. を押す
  
 I'm feeling lucky を押すと終了する
+
==== Step-5 ====
  うまくいかない場合もあるので、洒落です。
+
 I'm feeling lucky を押すと終了するが、予測したチェーン上書きされるので、チェーンの編集等をしたときには押してはいけない。
 +
 うまくいかない場合もあるので、洒落だと考えたほうがよい。
  
 
== 水の付加 ==
 
== 水の付加 ==
 
+
 水を周辺に配置する。
をつかって計算したいPDBファイルの大きさと位置を知る。
+
 
+
 
   VMD -> Extensions -> Modeling -> Add Solvate Box
 
   VMD -> Extensions -> Modeling -> Add Solvate Box
  
 
   もとになるPSF/PDBの読み込み
 
   もとになるPSF/PDBの読み込み
  Rotate to minimize volume をチェック
+
 Waterbox onlyのチェックを外す
    10/all 
+
 Rotate to minimize volume をチェック
  Output: 出力ファイルのベースネームを入力
+
    10/all 
 +
 もっと精確に向きを軸にそろえたいときは
 +
   1/all
 +
 +
 Output: 出力ファイルのベースネームを入力
  
 
 Segment ID Prefix: WT (そのままでよい)
 
 Segment ID Prefix: WT (そのままでよい)
 
 Boundary: 2.4 (そのままでよい)
 
 Boundary: 2.4 (そのままでよい)
 Box Size:  
+
  Box Size:  
   Min
+
    Min:  -40 -40 -40
  Max
+
    Max 40 40 40
  VMDの上で、分子の大きさは確認できる
+
   VMDの上で、分子の大きさは確認できる
   vmd: measure minmax [ atomselect top all]
+
     vmd: measure minmax [ atomselect top all]
  vmd: measure center [ atomselect top all]
+
   vmd: measure center [ atomselect top all]
 +
若しくは、Molecule Dimensionをチェックする。これにより、指定した分子に張り付いた形で水を配置できる。
 +
 
 +
  Pad Size: 周辺に水を配置する。Molcule Dimensionを設定した場合には、分子の周辺に水を拡げて配置できる.
 +
   Min: 10 10 10
 +
   Max: 10 10 10
  
 
 Solvateを押す
 
 Solvateを押す
 +
 +
== イオンの付加 ==
 +
 系全体を中性化すること、また、イオン強度を考慮するためにイオンを配置する。
 +
 +
  VMD -> Extensions -> Modeling -> Add Ions
 +
 +
  もとになるPSF/PDBの読み込み
 +
 +
Output prefix: 出力ファイルのベースネームを設定する
 +
Choose salt: 電解質(塩)の設定
 +
Ion placement mode: いずれかを選択する
 +
 Only neutralize system with NaCl    中性化のために最小限配置
 +
 Neutralize and set NaCl concentration to:  イオン強度の設定
 +
 User-defined number of ions:        イオン種毎に個数を設定する
 +
 +
Minimum distance from solute:
 +
Minimum distance between ions:
  
 
== namd.confの編集==
 
== namd.confの編集==
行182: 行223:
 
   
 
   
 
  run 2500 ;# 5ps
 
  run 2500 ;# 5ps
 +
 +
 +
== NAMD configuration file ==
 +
 +
<pre>
 +
NAMD configuration parameters
 +
Timestep parameters
 +
numsteps  $<$ number of timesteps $>$
 +
Acceptable Values: positive integer
 +
Description: The number of simulation timesteps to be performed. An integer greater than 0 is acceptable. The total amount of simulation time is $\mbox{{\tt numsteps}} \times \mbox{{\tt timestep}}$.
 +
timestep  $<$ timestep size (fs) $>$
 +
Acceptable Values: non-negative decimal
 +
Default Value: 1.0
 +
Description: The timestep size to use when integrating each step of the simulation. The value is specified in femtoseconds.
 +
firsttimestep  $<$ starting timestep value $>$
 +
Acceptable Values: non-negative integer
 +
Default Value: 0
 +
Description: The number of the first timestep. This value is typically used only when a simulation is a continuation of a previous simulation. In this case, rather than having the timestep restart at 0, a specific timestep number can be specified.
 +
stepspercycle  $<$ timesteps per cycle $>$
 +
Acceptable Values: positive integer
 +
Default Value: 20
 +
Description: Number of timesteps in each cycle. Each cycle represents the number of timesteps between atom reassignments. For more details on non-bonded force evaluation, see Section 5.1.
 +
Simulation space partitioning
 +
cutoff  $<$ local interaction distance common to both electrostatic and van der Waals calculations (Å) $>$
 +
Acceptable Values: positive decimal
 +
Description: See Section 5.1 for more information.
 +
switching  $<$ use switching function? $>$
 +
Acceptable Values: on or off
 +
Default Value: off
 +
Description: If switching is specified to be off, then a truncated cutoff is performed. If switching is turned on, then smoothing functions are applied to both the electrostatics and van der Waals forces. For a complete description of the non-bonded force parameters see Section 5.1. If switching is set to on, then switchdist must also be defined.
 +
switchdist  $<$ distance at which to activate switching function for electrostatic and van der Waals calculations (Å) $>$
 +
Acceptable Values: positive decimal $\leq$ cutoff
 +
Description: Distance at which the switching function should begin to take effect. This parameter only has meaning if switching is set to on. The value of switchdist must be less than or equal to the value of cutoff, since the switching function is only applied on the range from switchdist to cutoff. For a complete description of the non-bonded force parameters see Section 5.1.
 +
limitdist  $<$ maximum distance between pairs for limiting interaction strength(Å) $>$
 +
Acceptable Values: non-negative decimal
 +
Default Value: 0.
 +
Description: The electrostatic and van der Waals potential functions diverge as the distance between two atoms approaches zero. The potential for atoms closer than limitdist is instead treated as $a r^2 + c$ with parameters chosen to match the force and potential at limitdist. This option should primarily be useful for alchemical free energy perturbation calculations, since it makes the process of creating and destroying atoms far less drastic energetically. The larger the value of limitdist the more the maximum force between atoms will be reduced. In order to not alter the other interactions in the simulation, limitdist should be less than the closest approach of any non-bonded pair of atoms; 1.3Å appears to satisfy this for typical simulations but the user is encouraged to experiment. There should be no performance impact from enabling this feature.
 +
pairlistdist  $<$ distance between pairs for inclusion in pair lists (Å) $>$
 +
Acceptable Values: positive decimal $\geq$ cutoff
 +
Default Value: cutoff
 +
Description: A pair list is generated pairlistsPerCycle times each cycle, containing pairs of atoms for which electrostatics and van der Waals interactions will be calculated. This parameter is used when switching is set to on to specify the allowable distance between atoms for inclusion in the pair list. This parameter is equivalent to the X-PLOR parameter CUTNb. If no atom moves more than pairlistdist$-$cutoff during one cycle, then there will be no jump in electrostatic or van der Waals energies when the next pair list is built. Since such a jump is unavoidable when truncation is used, this parameter may only be specified when switching is set to on. If this parameter is not specified and switching is set to on, the value of cutoff is used. A value of at least one greater than cutoff is recommended.
 +
splitPatch  $<$ how to assign atoms to patches $>$
 +
Acceptable Values: position or hydrogen
 +
Default Value: hydrogen
 +
Description: When set to hydrogen, hydrogen atoms are kept on the same patch as their parents, allowing faster distance checking and rigid bonds.
 +
hgroupCutoff (Å)  $<$ used for group-based distance testing $>$
 +
Acceptable Values: positive decimal
 +
Default Value: 2.5
 +
Description: This should be set to twice the largest distance which will ever occur between a hydrogen atom and its mother. Warnings will be printed if this is not the case. This value is also added to the margin.
 +
margin  $<$ extra length in patch dimension (Å) $>$
 +
Acceptable Values: positive decimal
 +
Default Value: 0.0
 +
Description: An internal tuning parameter used in determining the size of the cubes of space with which NAMD uses to partition the system. The value of this parameter will not change the physical results of the simulation. Unless you are very motivated to get the very best possible performance, just leave this value at the default.
 +
pairlistMinProcs  $<$ min procs for pairlists $>$
 +
Acceptable Values: positive integer
 +
Default Value: 1
 +
Description: Pairlists may consume a large amount of memory as atom counts, densities, and cutoff distances increase. Since this data is distributed across processors it is normally only problematic for small processor counts. Set pairlistMinProcs to the smallest number of processors on which the simulation can fit into memory when pairlists are used.
 +
pairlistsPerCycle  $<$ regenerate x times per cycle $>$
 +
Acceptable Values: positive integer
 +
Default Value: 2
 +
Description: Rather than only regenerating the pairlist at the beginning of a cycle, regenerate multiple times in order to better balance the costs of atom migration, pairlist generation, and larger pairlists.
 +
outputPairlists  $<$ how often to print warnings $>$
 +
Acceptable Values: non-negative integer
 +
Default Value: 0
 +
Description: If an atom moves further than the pairlist tolerance during a simulation (initially (pairlistdist - cutoff)/2 but refined during the run) any pairlists covering that atom are invalidated and temporary pairlists are used until the next full pairlist regeneration. All interactions are calculated correctly, but efficiency may be degraded. Enabling outputPairlists will summarize these pairlist violation warnings periodically during the run.
 +
pairlistShrink  $<$ tol *= (1 - x) on regeneration $>$
 +
Acceptable Values: non-negative decimal
 +
Default Value: 0.01
 +
Description: In order to maintain validity for the pairlist for an entire cycle, the pairlist tolerance (the distance an atom can move without causing the pairlist to be invalidated) is adjusted during the simulation. Every time pairlists are regenerated the tolerance is reduced by this fraction.
 +
pairlistGrow  $<$ tol *= (1 + x) on trigger $>$
 +
Acceptable Values: non-negative decimal
 +
Default Value: 0.01
 +
Description: In order to maintain validity for the pairlist for an entire cycle, the pairlist tolerance (the distance an atom can move without causing the pairlist to be invalidated) is adjusted during the simulation. Every time an atom exceeds a trigger criterion that is some fraction of the tolerance distance, the tolerance is increased by this fraction.
 +
pairlistTrigger  $<$ trigger is atom beyond (1 - x) * tol $>$
 +
Acceptable Values: non-negative decimal
 +
Default Value: 0.3
 +
Description: The goal of pairlist tolerance adjustment is to make pairlist invalidations rare while keeping the tolerance as small as possible for best performance. Rather than monitoring the (very rare) case where atoms actually move more than the tolerance distance, we reduce the trigger tolerance by this fraction. The tolerance is increased whenever the trigger tolerance is exceeded, as specified by pairlistGrow.
 +
Basic dynamics
 +
exclude  $<$ exclusion policy to use $>$
 +
Acceptable Values: none, 1-2, 1-3, 1-4, or scaled1-4
 +
Description: This parameter specifies which pairs of bonded atoms should be excluded from non-bonded interactions. With the value of none, no bonded pairs of atoms will be excluded. With the value of 1-2, all atom pairs that are directly connected via a linear bond will be excluded. With the value of 1-3, all 1-2 pairs will be excluded along with all pairs of atoms that are bonded to a common third atom (i.e., if atom A is bonded to atom B and atom B is bonded to atom C, then the atom pair A-C would be excluded). With the value of 1-4, all 1-3 pairs will be excluded along with all pairs connected by a set of two bonds (i.e., if atom A is bonded to atom B, and atom B is bonded to atom C, and atom C is bonded to atom D, then the atom pair A-D would be excluded). With the value of scaled1-4, all 1-3 pairs are excluded and all pairs that match the 1-4 criteria are modified. The electrostatic interactions for such pairs are modified by the constant factor defined by 1-4scaling. The van der Waals interactions are modified by using the special 1-4 parameters defined in the parameter files.
 +
temperature  $<$ initial temperature (K) $>$
 +
Acceptable Values: positive decimal
 +
Description: Initial temperature value for the system. Using this option will generate a random velocity distribution for the initial velocities for all the atoms such that the system is at the desired temperature. Either the temperature or the velocities/binvelocities option must be defined to determine an initial set of velocities. Both options cannot be used together.
 +
COMmotion  $<$ allow initial center of mass motion? $>$
 +
Acceptable Values: yes or no
 +
Default Value: no
 +
Description: Specifies whether or not motion of the center of mass of the entire system is allowed. If this option is set to no, the initial velocities of the system will be adjusted to remove center of mass motion of the system. Note that this does not preclude later center-of-mass motion due to external forces such as random noise in Langevin dynamics, boundary potentials, and harmonic restraints.
 +
zeroMomentum  $<$ remove center of mass drift due to PME $>$
 +
Acceptable Values: yes or no
 +
Default Value: no
 +
Description: If enabled, the net momentum of the simulation and any resultant drift is removed before every full electrostatics step. This correction should conserve energy and have minimal impact on parallel scaling. This feature should only be used for simulations that would conserve momentum except for the slight errors in PME. (Features such as fixed atoms, harmonic restraints, steering forces, and Langevin dynamics do not conserve momentum; use in combination with these features should be considered experimental.) Since the momentum correction is delayed, enabling outputMomenta will show a slight nonzero linear momentum but there should be no center of mass drift.
 +
dielectric  $<$ dielectric constant for system $>$
 +
Acceptable Values: decimal $\geq$ 1.0
 +
Default Value: 1.0
 +
Description: Dielectric constant for the system. A value of 1.0 implies no modification of the electrostatic interactions. Any larger value will lessen the electrostatic forces acting in the system.
 +
1-4scaling  $<$ scaling factor for 1-4 interactions $>$
 +
Acceptable Values: 0 $\leq$ decimal $\leq$ 1
 +
Default Value: 1.0
 +
Description: Scaling factor for 1-4 interactions. This factor is only used when the exclude parameter is set to scaled1-4. In this case, this factor is used to modify the electrostatic interactions between 1-4 atom pairs. If the exclude parameter is set to anything but scaled1-4, this parameter has no effect regardless of its value.
 +
vdwGeometricSigma  $<$ use geometric mean to combine L-J sigmas $>$
 +
Acceptable Values: yes or no
 +
Default Value: no
 +
Description: Use geometric mean, as required by OPLS, rather than traditional arithmetic mean when combining Lennard-Jones sigma parameters for different atom types.
 +
seed  $<$ random number seed $>$
 +
Acceptable Values: positive integer
 +
Default Value: pseudo-random value based on current UNIX clock time
 +
Description: Number used to seed the random number generator if temperature or langevin is selected. This can be used so that consecutive simulations produce the same results. If no value is specified, NAMD will choose a pseudo-random value based on the current UNIX clock time. The random number seed will be output during the simulation startup so that its value is known and can be reused for subsequent simulations. Note that if Langevin dynamics are used in a parallel simulation (i.e., a simulation using more than one processor) even using the same seed will not guarantee reproducible results.
 +
rigidBonds  $<$ controls if and how ShakeH is used $>$
 +
Acceptable Values: none, water, all
 +
Default Value: none
 +
Description: When water is selected, the hydrogen-oxygen and hydrogen-hydrogen distances in waters are constrained to the nominal length or angle given in the parameter file, making the molecules completely rigid. When rigidBonds is all, waters are made rigid as described above and the bond between each hydrogen and the (one) atom to which it is bonded is similarly constrained. For the default case none, no lengths are constrained.
 +
rigidTolerance  $<$ allowable bond-length error for ShakeH (Å) $>$
 +
Acceptable Values: positive decimal
 +
Default Value: 1.0e-8
 +
Description: The ShakeH algorithm is assumed to have converged when all constrained bonds differ from the nominal bond length by less than this amount.
 +
rigidIterations  $<$ maximum ShakeH iterations $>$
 +
Acceptable Values: positive integer
 +
Default Value: 100
 +
Description: The maximum number of iterations ShakeH will perform before giving up on constraining the bond lengths. If the bond lengths do not converge, a warning message is printed, and the atoms are left at the final value achieved by ShakeH. Although the default value is 100, convergence is usually reached after fewer than 10 iterations.
 +
rigidDieOnError  $<$ maximum ShakeH iterations $>$
 +
Acceptable Values: on or off
 +
Default Value: on
 +
Description: Exit and report an error if rigidTolerance is not achieved after rigidIterations.
 +
useSettle  $<$ Use SETTLE for waters. $>$
 +
Acceptable Values: on or off
 +
Default Value: on
 +
Description: If rigidBonds are enabled then use the non-iterative SETTLE algorithm to keep waters rigid rather than the slower SHAKE algorithm.
 +
DPMTA parameters
 +
DPMTA is no longer included in the released NAMD binaries. We recommend that you instead use PME with a periodic system because it conserves energy better, is more efficient, and is better parallelized. If you must have the fast multipole algorithm you may compile NAMD yourself.
 +
 +
These parameters control the options to DPMTA, an algorithm used to provide full electrostatic interactions. DPMTA is a modified version of the FMA (Fast Multipole Algorithm) and, unfortunately, most of the parameters still refer to FMA rather than DPMTA for historical reasons. Don't be confused!
 +
 +
For a further description of how exactly full electrostatics are incorporated into NAMD, see Section 5.2. For a greater level of detail about DPMTA and the specific meaning of its options, see the DPMTA distribution which is available via anonymous FTP from the site ftp.ee.duke.edu in the directory /pub/SciComp/src.
 +
 +
FMA  $<$ use full electrostatics? $>$
 +
Acceptable Values: on or off
 +
Default Value: off
 +
Description: Specifies whether or not the DPMTA algorithm from Duke University should be used to compute the full electrostatic interactions. If set to on, DPMTA will be used with a multiple timestep integration scheme to provide full electrostatic interactions as detailed in Section 5.2. DPMTA is no longer included in released binaries.
 +
FMALevels  $<$ number of levels to use in multipole expansion $>$
 +
Acceptable Values: positive integer
 +
Default Value: 5
 +
Description: Number of levels to use for the multipole expansion. This parameter is only used if FMA is set to on. A value of 4 should be sufficient for systems with less than 10,000 atoms. A value of 5 or greater should be used for larger systems.
 +
FMAMp  $<$ number of multipole terms to use for FMA $>$
 +
Acceptable Values: positive integer
 +
Default Value: 8
 +
Description: Number of terms to use in the multipole expansion. This parameter is only used if FMA is set to on. If the FMAFFT is set to on, then this value must be a multiple of 4. The default value of 8 should be suitable for most applications.
 +
FMAFFT  $<$ use DPMTA FFT enhancement? $>$
 +
Acceptable Values: on or off
 +
Default Value: on
 +
Description: Specifies whether or not the DPMTA code should use the FFT enhancement feature. This parameter is only used if FMA is set to on. If FMAFFT is set to on, the value of FMAMp must be set to a multiple of 4. This feature offers substantial benefits only for values of FMAMp of 8 or greater. This feature will substantially increase the amount of memory used by DPMTA.
 +
FMAtheta  $<$ DPMTA theta parameter (radians) $>$
 +
Acceptable Values: decimal
 +
Default Value: 0.715
 +
Description: This parameter specifies the value of the theta parameter used in the DPMTA calculation. The default value is based on recommendations by the developers of the code.
 +
FMAFFTBlock  $<$ blocking factor for FMA FFT $>$
 +
Acceptable Values: positive integer
 +
Default Value: 4
 +
Description: The blocking factor for the FFT enhancement to DPMTA. This parameter is only used if both FMA and FMAFFT are set to on. The default value of 4 should be suitable for most applications.
 +
PME parameters
 +
PME stands for Particle Mesh Ewald and is an efficient full electrostatics method for use with periodic boundary conditions. None of the parameters should affect energy conservation, although they may affect the accuracy of the results and momentum conservation.
 +
 +
PME  $<$ Use particle mesh Ewald for electrostatics? $>$
 +
Acceptable Values: yes or no
 +
Default Value: no
 +
Description: Turns on particle mesh Ewald.
 +
PMETolerance  $<$ PME direct space tolerance $>$
 +
Acceptable Values: positive decimal
 +
Default Value:  $10^{-6}$
 +
Description: Affects the value of the Ewald coefficient and the overall accuracy of the results.
 +
PMEInterpOrder  $<$ PME interpolation order $>$
 +
Acceptable Values: positive integer
 +
Default Value: 4 (cubic)
 +
Description: Charges are interpolated onto the grid and forces are interpolated off using this many points, equal to the order of the interpolation function plus one.
 +
PMEGridSpacing  $<$ maximum space between grid points $>$
 +
Acceptable Values: positive real
 +
Description: The grid spacing partially determines the accuracy and efficiency of PME. If any of the grid sizes below are not set, then PMEGridSpacing must be set (recommended value is 1.0 Å) and will be used to calculate them. If a grid size is set, then the grid spacing must be at least PMEGridSpacing (if set, or a very large default of 1.5).
 +
PMEGridSizeX  $<$ number of grid points in x dimension $>$
 +
Acceptable Values: positive integer
 +
Description: The grid size partially determines the accuracy and efficiency of PME. For speed, PMEGridSizeX should have only small integer factors (2, 3 and 5).
 +
PMEGridSizeY  $<$ number of grid points in y dimension $>$
 +
Acceptable Values: positive integer
 +
Description: The grid size partially determines the accuracy and efficiency of PME. For speed, PMEGridSizeY should have only small integer factors (2, 3 and 5).
 +
PMEGridSizeZ  $<$ number of grid points in z dimension $>$
 +
Acceptable Values: positive integer
 +
Description: The grid size partially determines the accuracy and efficiency of PME. For speed, PMEGridSizeZ should have only small integer factors (2, 3 and 5).
 +
PMEProcessors  $<$ processors for FFT and reciprocal sum $>$
 +
Acceptable Values: positive integer
 +
Default Value: larger of x and y grid sizes up to all available processors
 +
Description: For best performance on some systems and machines, it may be necessary to restrict the amount of parallelism used. Experiment with this parameter if your parallel performance is poor when PME is used.
 +
FFTWEstimate  $<$ Use estimates to optimize FFT? $>$
 +
Acceptable Values: yes or no
 +
Default Value: no
 +
Description: Do not optimize FFT based on measurements, but on FFTW rules of thumb. This reduces startup time, but may affect performance.
 +
FFTWUseWisdom  $<$ Use FFTW wisdom archive file? $>$
 +
Acceptable Values: yes or no
 +
Default Value: yes
 +
Description: Try to reduce startup time when possible by reading FFTW ``wisdom'' from a file, and saving wisdom generated by performance measurements to the same file for future use. This will reduce startup time when running the same size PME grid on the same number of processors as a previous run using the same file.
 +
FFTWWisdomFile  $<$ name of file for FFTW wisdom archive $>$
 +
Acceptable Values: file name
 +
Default Value: FFTW_NAMD_version_platform.txt
 +
Description: File where FFTW wisdom is read and saved. If you only run on one platform this may be useful to reduce startup times for all runs. The default is likely sufficient, as it is version and platform specific.
 +
useDPME  $<$ Use old DPME code? $>$
 +
Acceptable Values: yes or no
 +
Default Value: no
 +
Description: Switches to old DPME implementation of particle mesh Ewald. The new code is faster and allows non-orthogonal cells so you probably just want to leave this option turned off. If you set cellOrigin to something other than $(0,0,0)$ the energy may differ slightly between the old and new implementations. DPME is no longer included in released binaries.
 +
Full direct parameters
 +
The direct computation of electrostatics is not intended to be used during real calculations, but rather as a testing or comparison measure. Because of the  ${\mathcal O}(N^2)$ computational complexity for performing direct calculations, this is much slower than using DPMTA or PME to compute full electrostatics for large systems. In the case of periodic boundary conditions, the nearest image convention is used rather than a full Ewald sum.
 +
 +
FullDirect  $<$ calculate full electrostatics directly? $>$
 +
Acceptable Values: yes or no
 +
Default Value: no
 +
Description: Specifies whether or not direct computation of full electrostatics should be performed.
 +
Multiple timestep parameters
 +
One of the areas of current research being studied using NAMD is the exploration of better methods for performing multiple timestep integration. Currently the only available method is the impulse-based Verlet-I or r-RESPA method which is stable for timesteps up to 4 fs for long-range electrostatic forces, 2 fs for short-range nonbonded forces, and 1 fs for bonded forces Setting rigid all (i.e., using SHAKE) increases these timesteps to 6 fs, 2 fs, and 2 fs respectively but eliminates bond motion for hydrogen. The mollified impulse method (MOLLY) reduces the resonance which limits the timesteps and thus increases these timesteps to 6 fs, 2 fs, and 1 fs while retaining all bond motion.
 +
 +
fullElectFrequency  $<$ number of timesteps between full electrostatic evaluations $>$
 +
Acceptable Values: positive integer factor of stepspercycle
 +
Default Value: nonbondedFreq
 +
Description: This parameter specifies the number of timesteps between each full electrostatics evaluation. It is recommended that fullElectFrequency be chosen so that the product of fullElectFrequency and timestep does not exceed $4.0$ unless rigidBonds all or molly on is specified, in which case the upper limit is perhaps doubled.
 +
nonbondedFreq  $<$ timesteps between nonbonded evaluation $>$
 +
Acceptable Values: positive integer factor of fullElectFrequency
 +
Default Value: 1
 +
Description: This parameter specifies how often short-range nonbonded interactions should be calculated. Setting nonbondedFreq between 1 and fullElectFrequency allows triple timestepping where, for example, one could evaluate bonded forces every 1 fs, short-range nonbonded forces every 2 fs, and long-range electrostatics every 4 fs.
 +
MTSAlgorithm  $<$ MTS algorithm to be used $>$
 +
Acceptable Values: impulse/verletI or constant/naive
 +
Default Value: impulse
 +
Description: Specifies the multiple timestep algorithm used to integrate the long and short range forces. impulse/verletI is the same as r-RESPA. constant/naive is the stale force extrapolation method.
 +
longSplitting  $<$ how should long and short range forces be split? $>$
 +
Acceptable Values: xplor, c1
 +
Default Value: c1
 +
Description: Specifies the method used to split electrostatic forces between long and short range potentials. The xplor option uses the X-PLOR shifting function, and the c1 splitting uses the following $C^1$ continuous shifting function [14]:
 +
$SW(r_{ij}) = 0$ if $\vert{{\vec{r}}_{ij}}\vert > R_{\mathit off}$
 +
$SW(r_{ij}) = 1$ if $\vert{{\vec{r}}_{ij}}\vert \leq R_{\mathit on}$
 +
if $R_{\mathit off} > \vert{{\vec{r}}_{ij}}\vert \geq R_{\mathit on}$
 +
where
 +
$R_{\mathit on}$ is a constant defined using the configuration value switchdist
 +
$R_{\mathit off}$ is specified using the configuration value cutoff
 +
molly  $<$ use mollified impulse method (MOLLY)? $>$
 +
Acceptable Values: on or off
 +
Default Value: off
 +
Description: This method eliminates the components of the long range electrostatic forces which contribute to resonance along bonds to hydrogen atoms, allowing a fullElectFrequency of 6 (vs. 4) with a 1 fs timestep without using rigidBonds all. You may use rigidBonds water but using rigidBonds all with MOLLY makes no sense since the degrees of freedom which MOLLY protects from resonance are already frozen.
 +
mollyTolerance  $<$ allowable error for MOLLY $>$
 +
Acceptable Values: positive decimal
 +
Default Value: 0.00001
 +
Description: Convergence criterion for MOLLY algorithm.
 +
mollyIterations  $<$ maximum MOLLY iterations $>$
 +
Acceptable Values: positive integer
 +
Default Value: 100
 +
Description: Maximum number of iterations for MOLLY algorithm.
 +
 +
</pre>

2018年2月1日 (木) 07:16時点における最新版

'NAMD'の利用の仕方をまとめておきます。

PDBファイルの取得

データベースからダウンロード

 データベース先:https://www.rcsb.org/pdb/home/home.do

水素の付加

 Chimera Tools -> Structture Edition -> AddHで実施

水の排除

  psfファイルを作成する際に、水を除いておく必要がある。

 PDBファイルを詠み込んで、分子を選択した後,File -> Save Coordinatresで保存   このとき、

 selected atoms: を設定する
 selected atoms: protein (タンパク質のみ選択)
 selected atoms: nucleic  (DNAのみを選択)
 selected atoms: not water (水以外を選択)
 selected atoms: not water and not protein (水とタンパク質以外を選択)
 File type:  PDB
 Save ボタンで保存

PSFファイルの作成

VMD を利用

PDBファイルの読み込み

Extensions -> Modeling -> Automatic PSF Builder

Step-1: Input and Output Files

分子の選択をして下さい。

 Molecule

出力用のベースネームを設定して下さい。

 output basename: 

 出力ファイルのベースネーム(.pdb/.psfを除いたもの)

  ディレクトリがずれていると出力がうまくいかない事があるので、vmd consoleでcdで移動するか、もしくは、Output basenameにディレクトリ毎指定する必要がある)   Topologyファイルの選択(通常はデフォールトでよい)   Load input filesを押す

Step-2: Selections to include in PSF/PDB

  Everything(default) (ここで、たんぱく質(protein)と核酸(Nucleic acid)の選択も可能)
  Guess and split chains using current selections を押す

  内部にはいっているチェーンがStep-3のウィンドウで確認できる   2本鎖DNAの場合は,2つのチェーンが確認できます.   編集したい場合は、こちらで編集  

Step-3:

  チェーン(共有結合でつながっているもの)の編集が必要なら行う

  Create chainsを押す

Step-4:

  patch(つなぎ合わせ)が必要なら行う。

  Apply patches and finish PSF/PDB. を押す

Step-5

 I'm feeling lucky を押すと終了するが、予測したチェーン上書きされるので、チェーンの編集等をしたときには押してはいけない。  うまくいかない場合もあるので、洒落だと考えたほうがよい。

水の付加

 水を周辺に配置する。

 VMD -> Extensions -> Modeling -> Add Solvate Box
 もとになるPSF/PDBの読み込み

 Waterbox onlyのチェックを外す  Rotate to minimize volume をチェック

    10/all 

 もっと精確に向きを軸にそろえたいときは

   1/all

 Output: 出力ファイルのベースネームを入力

 Segment ID Prefix: WT (そのままでよい)  Boundary: 2.4 (そのままでよい)

 Box Size: 
   Min:  -40 -40 -40 
   Max  40 40 40 

  VMDの上で、分子の大きさは確認できる

   vmd: measure minmax [ atomselect top all]
   vmd: measure center [ atomselect top all]

若しくは、Molecule Dimensionをチェックする。これにより、指定した分子に張り付いた形で水を配置できる。

 Pad Size: 周辺に水を配置する。Molcule Dimensionを設定した場合には、分子の周辺に水を拡げて配置できる.
  Min: 10 10 10
  Max: 10 10 10

 Solvateを押す

イオンの付加

 系全体を中性化すること、また、イオン強度を考慮するためにイオンを配置する。

 VMD -> Extensions -> Modeling -> Add Ions
 もとになるPSF/PDBの読み込み
Output prefix: 出力ファイルのベースネームを設定する
Choose salt: 電解質(塩)の設定
Ion placement mode: いずれかを選択する
 Only neutralize system with NaCl    中性化のために最小限配置
 Neutralize and set NaCl concentration to:   イオン強度の設定
 User-defined number of ions:        イオン種毎に個数を設定する 
Minimum distance from solute:
Minimum distance between ions:

namd.confの編集

#############################################################
## JOB DESCRIPTION                                         ##
############################################################# 

# Minimization and Equilibration of 
# Ubiquitin in a Water Box


#############################################################
## ADJUSTABLE PARAMETERS                                   ##
#############################################################

structure          dna-HOH+H_autopsf+HOH.pdb.psf 
coordinates        dna-HOH+H_autopsf+HOH.pdb.pdb

#変数宣言
set temperature    310
set outputname     dnaW_eq+HOH

firsttimestep      0


#############################################################
## SIMULATION PARAMETERS                                   ##
#############################################################

# Input
paraTypeCharmm	    on
#parameters          par_all27_prot_lipid.inp 
#parameters          par_all22_prot_na.inp 
parameters          charmm/test/data/par_all36_na_mod.prm 
temperature         $temperature


# Force-Field Parameters
exclude             scaled1-4
1-4scaling          1.0
cutoff              12.0
switching           on
switchdist          10.0
pairlistdist        14.0


# Integrator Parameters
timestep            1.0  ;# 2fs/step
rigidBonds          all  ;# needed for 2fs steps
nonbondedFreq       1
fullElectFrequency  2  
stepspercycle       10


# Constant Temperature Control
langevin            on    ;# do langevin dynamics
langevinDamping     1     ;# damping coefficient (gamma) of 1/ps
langevinTemp        $temperature
langevinHydrogen    off    ;# don't couple langevin bath to hydrogens


# Periodic Boundary Conditions
cellBasisVector1    200.0,0.0,0.0
cellBasisVector2     0.0,200.0,0.0
cellBasisVector3     0.0,0.0,240.0
cellOrigin           14.0,0.0,-20.0

wrapAll             on


# PME (for full-system periodic electrostatics)
PME                 yes
PMEGridSpacing      1.0

#manual grid definition
#PMEGridSizeX        45
#PMEGridSizeY        45
#PMEGridSizeZ        48


# Constant Pressure Control (variable volume)
useGroupPressure      yes ;# needed for rigidBonds
useFlexibleCell       yes 
 
useConstantArea       no

langevinPiston        on
langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
langevinPistonPeriod  100.0
langevinPistonDecay   50.0
langevinPistonTemp    $temperature 


# Output
outputName          $outputname

restartfreq         500     ;# 500steps = every 1ps
dcdfreq             100
xstFreq             100 
outputEnergies      100
outputPressure      100


#############################################################
## EXTRA PARAMETERS                                        ##
#############################################################


#############################################################
## EXECUTION SCRIPT                                        ##
#############################################################

# Minimization
minimize            100
reinitvels          $temperature

run 2500 ;# 5ps


NAMD configuration file

NAMD configuration parameters
Timestep parameters
numsteps  $<$ number of timesteps $>$ 
Acceptable Values: positive integer 
Description: The number of simulation timesteps to be performed. An integer greater than 0 is acceptable. The total amount of simulation time is $\mbox{{\tt numsteps}} \times \mbox{{\tt timestep}}$.
timestep  $<$ timestep size (fs) $>$ 
Acceptable Values: non-negative decimal 
Default Value: 1.0 
Description: The timestep size to use when integrating each step of the simulation. The value is specified in femtoseconds.
firsttimestep  $<$ starting timestep value $>$ 
Acceptable Values: non-negative integer 
Default Value: 0 
Description: The number of the first timestep. This value is typically used only when a simulation is a continuation of a previous simulation. In this case, rather than having the timestep restart at 0, a specific timestep number can be specified.
stepspercycle  $<$ timesteps per cycle $>$ 
Acceptable Values: positive integer 
Default Value: 20 
Description: Number of timesteps in each cycle. Each cycle represents the number of timesteps between atom reassignments. For more details on non-bonded force evaluation, see Section 5.1.
Simulation space partitioning
cutoff  $<$ local interaction distance common to both electrostatic and van der Waals calculations (Å) $>$ 
Acceptable Values: positive decimal 
Description: See Section 5.1 for more information.
switching  $<$ use switching function? $>$ 
Acceptable Values: on or off 
Default Value: off 
Description: If switching is specified to be off, then a truncated cutoff is performed. If switching is turned on, then smoothing functions are applied to both the electrostatics and van der Waals forces. For a complete description of the non-bonded force parameters see Section 5.1. If switching is set to on, then switchdist must also be defined.
switchdist  $<$ distance at which to activate switching function for electrostatic and van der Waals calculations (Å) $>$ 
Acceptable Values: positive decimal $\leq$ cutoff 
Description: Distance at which the switching function should begin to take effect. This parameter only has meaning if switching is set to on. The value of switchdist must be less than or equal to the value of cutoff, since the switching function is only applied on the range from switchdist to cutoff. For a complete description of the non-bonded force parameters see Section 5.1.
limitdist  $<$ maximum distance between pairs for limiting interaction strength(Å) $>$ 
Acceptable Values: non-negative decimal 
Default Value: 0. 
Description: The electrostatic and van der Waals potential functions diverge as the distance between two atoms approaches zero. The potential for atoms closer than limitdist is instead treated as $a r^2 + c$ with parameters chosen to match the force and potential at limitdist. This option should primarily be useful for alchemical free energy perturbation calculations, since it makes the process of creating and destroying atoms far less drastic energetically. The larger the value of limitdist the more the maximum force between atoms will be reduced. In order to not alter the other interactions in the simulation, limitdist should be less than the closest approach of any non-bonded pair of atoms; 1.3Å appears to satisfy this for typical simulations but the user is encouraged to experiment. There should be no performance impact from enabling this feature.
pairlistdist  $<$ distance between pairs for inclusion in pair lists (Å) $>$ 
Acceptable Values: positive decimal $\geq$ cutoff 
Default Value: cutoff 
Description: A pair list is generated pairlistsPerCycle times each cycle, containing pairs of atoms for which electrostatics and van der Waals interactions will be calculated. This parameter is used when switching is set to on to specify the allowable distance between atoms for inclusion in the pair list. This parameter is equivalent to the X-PLOR parameter CUTNb. If no atom moves more than pairlistdist$-$cutoff during one cycle, then there will be no jump in electrostatic or van der Waals energies when the next pair list is built. Since such a jump is unavoidable when truncation is used, this parameter may only be specified when switching is set to on. If this parameter is not specified and switching is set to on, the value of cutoff is used. A value of at least one greater than cutoff is recommended.
splitPatch  $<$ how to assign atoms to patches $>$ 
Acceptable Values: position or hydrogen 
Default Value: hydrogen 
Description: When set to hydrogen, hydrogen atoms are kept on the same patch as their parents, allowing faster distance checking and rigid bonds.
hgroupCutoff (Å)  $<$ used for group-based distance testing $>$ 
Acceptable Values: positive decimal 
Default Value: 2.5 
Description: This should be set to twice the largest distance which will ever occur between a hydrogen atom and its mother. Warnings will be printed if this is not the case. This value is also added to the margin.
margin  $<$ extra length in patch dimension (Å) $>$ 
Acceptable Values: positive decimal 
Default Value: 0.0 
Description: An internal tuning parameter used in determining the size of the cubes of space with which NAMD uses to partition the system. The value of this parameter will not change the physical results of the simulation. Unless you are very motivated to get the very best possible performance, just leave this value at the default.
pairlistMinProcs  $<$ min procs for pairlists $>$ 
Acceptable Values: positive integer 
Default Value: 1 
Description: Pairlists may consume a large amount of memory as atom counts, densities, and cutoff distances increase. Since this data is distributed across processors it is normally only problematic for small processor counts. Set pairlistMinProcs to the smallest number of processors on which the simulation can fit into memory when pairlists are used.
pairlistsPerCycle  $<$ regenerate x times per cycle $>$ 
Acceptable Values: positive integer 
Default Value: 2 
Description: Rather than only regenerating the pairlist at the beginning of a cycle, regenerate multiple times in order to better balance the costs of atom migration, pairlist generation, and larger pairlists.
outputPairlists  $<$ how often to print warnings $>$ 
Acceptable Values: non-negative integer 
Default Value: 0 
Description: If an atom moves further than the pairlist tolerance during a simulation (initially (pairlistdist - cutoff)/2 but refined during the run) any pairlists covering that atom are invalidated and temporary pairlists are used until the next full pairlist regeneration. All interactions are calculated correctly, but efficiency may be degraded. Enabling outputPairlists will summarize these pairlist violation warnings periodically during the run.
pairlistShrink  $<$ tol *= (1 - x) on regeneration $>$ 
Acceptable Values: non-negative decimal 
Default Value: 0.01 
Description: In order to maintain validity for the pairlist for an entire cycle, the pairlist tolerance (the distance an atom can move without causing the pairlist to be invalidated) is adjusted during the simulation. Every time pairlists are regenerated the tolerance is reduced by this fraction.
pairlistGrow  $<$ tol *= (1 + x) on trigger $>$ 
Acceptable Values: non-negative decimal 
Default Value: 0.01 
Description: In order to maintain validity for the pairlist for an entire cycle, the pairlist tolerance (the distance an atom can move without causing the pairlist to be invalidated) is adjusted during the simulation. Every time an atom exceeds a trigger criterion that is some fraction of the tolerance distance, the tolerance is increased by this fraction.
pairlistTrigger  $<$ trigger is atom beyond (1 - x) * tol $>$ 
Acceptable Values: non-negative decimal 
Default Value: 0.3 
Description: The goal of pairlist tolerance adjustment is to make pairlist invalidations rare while keeping the tolerance as small as possible for best performance. Rather than monitoring the (very rare) case where atoms actually move more than the tolerance distance, we reduce the trigger tolerance by this fraction. The tolerance is increased whenever the trigger tolerance is exceeded, as specified by pairlistGrow.
Basic dynamics
exclude  $<$ exclusion policy to use $>$ 
Acceptable Values: none, 1-2, 1-3, 1-4, or scaled1-4 
Description: This parameter specifies which pairs of bonded atoms should be excluded from non-bonded interactions. With the value of none, no bonded pairs of atoms will be excluded. With the value of 1-2, all atom pairs that are directly connected via a linear bond will be excluded. With the value of 1-3, all 1-2 pairs will be excluded along with all pairs of atoms that are bonded to a common third atom (i.e., if atom A is bonded to atom B and atom B is bonded to atom C, then the atom pair A-C would be excluded). With the value of 1-4, all 1-3 pairs will be excluded along with all pairs connected by a set of two bonds (i.e., if atom A is bonded to atom B, and atom B is bonded to atom C, and atom C is bonded to atom D, then the atom pair A-D would be excluded). With the value of scaled1-4, all 1-3 pairs are excluded and all pairs that match the 1-4 criteria are modified. The electrostatic interactions for such pairs are modified by the constant factor defined by 1-4scaling. The van der Waals interactions are modified by using the special 1-4 parameters defined in the parameter files.
temperature  $<$ initial temperature (K) $>$ 
Acceptable Values: positive decimal 
Description: Initial temperature value for the system. Using this option will generate a random velocity distribution for the initial velocities for all the atoms such that the system is at the desired temperature. Either the temperature or the velocities/binvelocities option must be defined to determine an initial set of velocities. Both options cannot be used together.
COMmotion  $<$ allow initial center of mass motion? $>$ 
Acceptable Values: yes or no 
Default Value: no 
Description: Specifies whether or not motion of the center of mass of the entire system is allowed. If this option is set to no, the initial velocities of the system will be adjusted to remove center of mass motion of the system. Note that this does not preclude later center-of-mass motion due to external forces such as random noise in Langevin dynamics, boundary potentials, and harmonic restraints.
zeroMomentum  $<$ remove center of mass drift due to PME $>$ 
Acceptable Values: yes or no 
Default Value: no 
Description: If enabled, the net momentum of the simulation and any resultant drift is removed before every full electrostatics step. This correction should conserve energy and have minimal impact on parallel scaling. This feature should only be used for simulations that would conserve momentum except for the slight errors in PME. (Features such as fixed atoms, harmonic restraints, steering forces, and Langevin dynamics do not conserve momentum; use in combination with these features should be considered experimental.) Since the momentum correction is delayed, enabling outputMomenta will show a slight nonzero linear momentum but there should be no center of mass drift.
dielectric  $<$ dielectric constant for system $>$ 
Acceptable Values: decimal $\geq$ 1.0 
Default Value: 1.0 
Description: Dielectric constant for the system. A value of 1.0 implies no modification of the electrostatic interactions. Any larger value will lessen the electrostatic forces acting in the system.
1-4scaling  $<$ scaling factor for 1-4 interactions $>$ 
Acceptable Values: 0 $\leq$ decimal $\leq$ 1 
Default Value: 1.0 
Description: Scaling factor for 1-4 interactions. This factor is only used when the exclude parameter is set to scaled1-4. In this case, this factor is used to modify the electrostatic interactions between 1-4 atom pairs. If the exclude parameter is set to anything but scaled1-4, this parameter has no effect regardless of its value.
vdwGeometricSigma  $<$ use geometric mean to combine L-J sigmas $>$ 
Acceptable Values: yes or no 
Default Value: no 
Description: Use geometric mean, as required by OPLS, rather than traditional arithmetic mean when combining Lennard-Jones sigma parameters for different atom types.
seed  $<$ random number seed $>$ 
Acceptable Values: positive integer 
Default Value: pseudo-random value based on current UNIX clock time 
Description: Number used to seed the random number generator if temperature or langevin is selected. This can be used so that consecutive simulations produce the same results. If no value is specified, NAMD will choose a pseudo-random value based on the current UNIX clock time. The random number seed will be output during the simulation startup so that its value is known and can be reused for subsequent simulations. Note that if Langevin dynamics are used in a parallel simulation (i.e., a simulation using more than one processor) even using the same seed will not guarantee reproducible results.
rigidBonds  $<$ controls if and how ShakeH is used $>$ 
Acceptable Values: none, water, all 
Default Value: none 
Description: When water is selected, the hydrogen-oxygen and hydrogen-hydrogen distances in waters are constrained to the nominal length or angle given in the parameter file, making the molecules completely rigid. When rigidBonds is all, waters are made rigid as described above and the bond between each hydrogen and the (one) atom to which it is bonded is similarly constrained. For the default case none, no lengths are constrained.
rigidTolerance  $<$ allowable bond-length error for ShakeH (Å) $>$ 
Acceptable Values: positive decimal 
Default Value: 1.0e-8 
Description: The ShakeH algorithm is assumed to have converged when all constrained bonds differ from the nominal bond length by less than this amount.
rigidIterations  $<$ maximum ShakeH iterations $>$ 
Acceptable Values: positive integer 
Default Value: 100 
Description: The maximum number of iterations ShakeH will perform before giving up on constraining the bond lengths. If the bond lengths do not converge, a warning message is printed, and the atoms are left at the final value achieved by ShakeH. Although the default value is 100, convergence is usually reached after fewer than 10 iterations.
rigidDieOnError  $<$ maximum ShakeH iterations $>$ 
Acceptable Values: on or off 
Default Value: on 
Description: Exit and report an error if rigidTolerance is not achieved after rigidIterations.
useSettle  $<$ Use SETTLE for waters. $>$ 
Acceptable Values: on or off 
Default Value: on 
Description: If rigidBonds are enabled then use the non-iterative SETTLE algorithm to keep waters rigid rather than the slower SHAKE algorithm.
DPMTA parameters
DPMTA is no longer included in the released NAMD binaries. We recommend that you instead use PME with a periodic system because it conserves energy better, is more efficient, and is better parallelized. If you must have the fast multipole algorithm you may compile NAMD yourself.

These parameters control the options to DPMTA, an algorithm used to provide full electrostatic interactions. DPMTA is a modified version of the FMA (Fast Multipole Algorithm) and, unfortunately, most of the parameters still refer to FMA rather than DPMTA for historical reasons. Don't be confused!

For a further description of how exactly full electrostatics are incorporated into NAMD, see Section 5.2. For a greater level of detail about DPMTA and the specific meaning of its options, see the DPMTA distribution which is available via anonymous FTP from the site ftp.ee.duke.edu in the directory /pub/SciComp/src.

FMA  $<$ use full electrostatics? $>$ 
Acceptable Values: on or off 
Default Value: off 
Description: Specifies whether or not the DPMTA algorithm from Duke University should be used to compute the full electrostatic interactions. If set to on, DPMTA will be used with a multiple timestep integration scheme to provide full electrostatic interactions as detailed in Section 5.2. DPMTA is no longer included in released binaries.
FMALevels  $<$ number of levels to use in multipole expansion $>$ 
Acceptable Values: positive integer 
Default Value: 5 
Description: Number of levels to use for the multipole expansion. This parameter is only used if FMA is set to on. A value of 4 should be sufficient for systems with less than 10,000 atoms. A value of 5 or greater should be used for larger systems.
FMAMp  $<$ number of multipole terms to use for FMA $>$ 
Acceptable Values: positive integer 
Default Value: 8 
Description: Number of terms to use in the multipole expansion. This parameter is only used if FMA is set to on. If the FMAFFT is set to on, then this value must be a multiple of 4. The default value of 8 should be suitable for most applications.
FMAFFT  $<$ use DPMTA FFT enhancement? $>$ 
Acceptable Values: on or off 
Default Value: on 
Description: Specifies whether or not the DPMTA code should use the FFT enhancement feature. This parameter is only used if FMA is set to on. If FMAFFT is set to on, the value of FMAMp must be set to a multiple of 4. This feature offers substantial benefits only for values of FMAMp of 8 or greater. This feature will substantially increase the amount of memory used by DPMTA.
FMAtheta  $<$ DPMTA theta parameter (radians) $>$ 
Acceptable Values: decimal 
Default Value: 0.715 
Description: This parameter specifies the value of the theta parameter used in the DPMTA calculation. The default value is based on recommendations by the developers of the code.
FMAFFTBlock  $<$ blocking factor for FMA FFT $>$ 
Acceptable Values: positive integer 
Default Value: 4 
Description: The blocking factor for the FFT enhancement to DPMTA. This parameter is only used if both FMA and FMAFFT are set to on. The default value of 4 should be suitable for most applications.
PME parameters
PME stands for Particle Mesh Ewald and is an efficient full electrostatics method for use with periodic boundary conditions. None of the parameters should affect energy conservation, although they may affect the accuracy of the results and momentum conservation.

PME  $<$ Use particle mesh Ewald for electrostatics? $>$ 
Acceptable Values: yes or no 
Default Value: no 
Description: Turns on particle mesh Ewald.
PMETolerance  $<$ PME direct space tolerance $>$ 
Acceptable Values: positive decimal 
Default Value:  $10^{-6}$ 
Description: Affects the value of the Ewald coefficient and the overall accuracy of the results.
PMEInterpOrder  $<$ PME interpolation order $>$ 
Acceptable Values: positive integer 
Default Value: 4 (cubic) 
Description: Charges are interpolated onto the grid and forces are interpolated off using this many points, equal to the order of the interpolation function plus one.
PMEGridSpacing  $<$ maximum space between grid points $>$ 
Acceptable Values: positive real 
Description: The grid spacing partially determines the accuracy and efficiency of PME. If any of the grid sizes below are not set, then PMEGridSpacing must be set (recommended value is 1.0 Å) and will be used to calculate them. If a grid size is set, then the grid spacing must be at least PMEGridSpacing (if set, or a very large default of 1.5).
PMEGridSizeX  $<$ number of grid points in x dimension $>$ 
Acceptable Values: positive integer 
Description: The grid size partially determines the accuracy and efficiency of PME. For speed, PMEGridSizeX should have only small integer factors (2, 3 and 5).
PMEGridSizeY  $<$ number of grid points in y dimension $>$ 
Acceptable Values: positive integer 
Description: The grid size partially determines the accuracy and efficiency of PME. For speed, PMEGridSizeY should have only small integer factors (2, 3 and 5).
PMEGridSizeZ  $<$ number of grid points in z dimension $>$ 
Acceptable Values: positive integer 
Description: The grid size partially determines the accuracy and efficiency of PME. For speed, PMEGridSizeZ should have only small integer factors (2, 3 and 5).
PMEProcessors  $<$ processors for FFT and reciprocal sum $>$ 
Acceptable Values: positive integer 
Default Value: larger of x and y grid sizes up to all available processors 
Description: For best performance on some systems and machines, it may be necessary to restrict the amount of parallelism used. Experiment with this parameter if your parallel performance is poor when PME is used.
FFTWEstimate  $<$ Use estimates to optimize FFT? $>$ 
Acceptable Values: yes or no 
Default Value: no 
Description: Do not optimize FFT based on measurements, but on FFTW rules of thumb. This reduces startup time, but may affect performance.
FFTWUseWisdom  $<$ Use FFTW wisdom archive file? $>$ 
Acceptable Values: yes or no 
Default Value: yes 
Description: Try to reduce startup time when possible by reading FFTW ``wisdom'' from a file, and saving wisdom generated by performance measurements to the same file for future use. This will reduce startup time when running the same size PME grid on the same number of processors as a previous run using the same file.
FFTWWisdomFile  $<$ name of file for FFTW wisdom archive $>$ 
Acceptable Values: file name 
Default Value: FFTW_NAMD_version_platform.txt 
Description: File where FFTW wisdom is read and saved. If you only run on one platform this may be useful to reduce startup times for all runs. The default is likely sufficient, as it is version and platform specific.
useDPME  $<$ Use old DPME code? $>$ 
Acceptable Values: yes or no 
Default Value: no 
Description: Switches to old DPME implementation of particle mesh Ewald. The new code is faster and allows non-orthogonal cells so you probably just want to leave this option turned off. If you set cellOrigin to something other than $(0,0,0)$ the energy may differ slightly between the old and new implementations. DPME is no longer included in released binaries.
Full direct parameters
The direct computation of electrostatics is not intended to be used during real calculations, but rather as a testing or comparison measure. Because of the  ${\mathcal O}(N^2)$ computational complexity for performing direct calculations, this is much slower than using DPMTA or PME to compute full electrostatics for large systems. In the case of periodic boundary conditions, the nearest image convention is used rather than a full Ewald sum.

FullDirect  $<$ calculate full electrostatics directly? $>$ 
Acceptable Values: yes or no 
Default Value: no 
Description: Specifies whether or not direct computation of full electrostatics should be performed.
Multiple timestep parameters
One of the areas of current research being studied using NAMD is the exploration of better methods for performing multiple timestep integration. Currently the only available method is the impulse-based Verlet-I or r-RESPA method which is stable for timesteps up to 4 fs for long-range electrostatic forces, 2 fs for short-range nonbonded forces, and 1 fs for bonded forces Setting rigid all (i.e., using SHAKE) increases these timesteps to 6 fs, 2 fs, and 2 fs respectively but eliminates bond motion for hydrogen. The mollified impulse method (MOLLY) reduces the resonance which limits the timesteps and thus increases these timesteps to 6 fs, 2 fs, and 1 fs while retaining all bond motion.

fullElectFrequency  $<$ number of timesteps between full electrostatic evaluations $>$ 
Acceptable Values: positive integer factor of stepspercycle 
Default Value: nonbondedFreq 
Description: This parameter specifies the number of timesteps between each full electrostatics evaluation. It is recommended that fullElectFrequency be chosen so that the product of fullElectFrequency and timestep does not exceed $4.0$ unless rigidBonds all or molly on is specified, in which case the upper limit is perhaps doubled.
nonbondedFreq  $<$ timesteps between nonbonded evaluation $>$ 
Acceptable Values: positive integer factor of fullElectFrequency 
Default Value: 1 
Description: This parameter specifies how often short-range nonbonded interactions should be calculated. Setting nonbondedFreq between 1 and fullElectFrequency allows triple timestepping where, for example, one could evaluate bonded forces every 1 fs, short-range nonbonded forces every 2 fs, and long-range electrostatics every 4 fs.
MTSAlgorithm  $<$ MTS algorithm to be used $>$ 
Acceptable Values: impulse/verletI or constant/naive 
Default Value: impulse 
Description: Specifies the multiple timestep algorithm used to integrate the long and short range forces. impulse/verletI is the same as r-RESPA. constant/naive is the stale force extrapolation method.
longSplitting  $<$ how should long and short range forces be split? $>$ 
Acceptable Values: xplor, c1 
Default Value: c1 
Description: Specifies the method used to split electrostatic forces between long and short range potentials. The xplor option uses the X-PLOR shifting function, and the c1 splitting uses the following $C^1$ continuous shifting function [14]:
$SW(r_{ij}) = 0$ if $\vert{{\vec{r}}_{ij}}\vert > R_{\mathit off}$
$SW(r_{ij}) = 1$ if $\vert{{\vec{r}}_{ij}}\vert \leq R_{\mathit on}$
if $R_{\mathit off} > \vert{{\vec{r}}_{ij}}\vert \geq R_{\mathit on}$
where
$R_{\mathit on}$ is a constant defined using the configuration value switchdist
$R_{\mathit off}$ is specified using the configuration value cutoff
molly  $<$ use mollified impulse method (MOLLY)? $>$ 
Acceptable Values: on or off 
Default Value: off 
Description: This method eliminates the components of the long range electrostatic forces which contribute to resonance along bonds to hydrogen atoms, allowing a fullElectFrequency of 6 (vs. 4) with a 1 fs timestep without using rigidBonds all. You may use rigidBonds water but using rigidBonds all with MOLLY makes no sense since the degrees of freedom which MOLLY protects from resonance are already frozen.
mollyTolerance  $<$ allowable error for MOLLY $>$ 
Acceptable Values: positive decimal 
Default Value: 0.00001 
Description: Convergence criterion for MOLLY algorithm.
mollyIterations  $<$ maximum MOLLY iterations $>$ 
Acceptable Values: positive integer 
Default Value: 100 
Description: Maximum number of iterations for MOLLY algorithm.