「NAMD」の版間の差分
(ページの作成:「'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...」) |
(→namd.confの編集) |
||
行48: | 行48: | ||
== namd.confの編集== | == 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 |
2017年12月18日 (月) 05:26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