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(namd.confの編集)
(namd.confの編集)
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== namd.confの編集==
 
== namd.confの編集==
#############################################################
+
#############################################################
## JOB DESCRIPTION                                        ##
+
## 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
 +
 +
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
  
# Minimization and Equilibration of
+
 
# Ubiquitin in a Water Box
+
#############################################################
 
+
## EXTRA PARAMETERS                                       ##
 
+
#############################################################
#############################################################
+
## ADJUSTABLE PARAMETERS                                   ##
+
#############################################################
+
 
+
structure          dna-HOH+H_autopsf+HOH.pdb.psf
+
coordinates        dna-HOH+H_autopsf+HOH.pdb.pdb
+
 
+
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
+
## EXECUTION SCRIPT                                        ##
langevinPistonTarget 1.01325 ;#  in bar -> 1 atm
+
#############################################################
langevinPistonPeriod 100.0
+
langevinPistonDecay  50.0
+
# Minimization
langevinPistonTemp    $temperature
+
minimize            100
 
+
reinitvels          $temperature
 
+
# Output
+
run 2500 ;# 5ps
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
+

2017年12月18日 (月) 05:29時点における版

'NAMD'の利用の仕方をまとめておきます。

PDBファイルの取得

 水を除く

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:Molecule
  output basename: 出力ファイルのベースネーム(.pdb/.psfを除いたもの)

  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:

  Everything(default)
  Guess and split chains using current selections を押す
 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

 I'm feeling lucky を押すと終了する   うまくいかない場合もあるので、洒落です。


水の付加

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

  Rotate to minimize volume をチェック     10/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
  Max
  VMDの上で、分子の大きさは確認できる

 Solvateを押す

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

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