NAMD-note
Namd2-gpu +p20 conf > log
charm_run ++nodelist nodelist namd_2 +p80 ++ppn 20 ../../../ante/allff3/complex_popc/namd/prod_test3/prod8.conf > ../../../ante/allff3/complex_popc/namd/prod_test3/prod8.log &
Minimize’Configuration file：
可調參數：
amber on
parmfile ../complex_0.1.prmtop
ambercoor ../prod1.rst7
#structure mypsf.psf
#coordinates mypdb.pdb
#outputName myoutput
set temperature 300 ;#結構優化時設置沒用，但是得有個
set outputname ./prod_2
firsttimestep 0
# Continuing a job from the restart files
if {0} { ;#最小化用不到輸入文件，所以設置為不啟用
set inputname proding_2
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel ;# remove the "temperature" entry if you use this!
extendedSystem $inputname.xsc
}
模擬參數：
# Input
#paraTypeCharmm on
#parameters par_all27_prot_lipid.inp
# NOTE: Do not set the initial velocity temperature if you
# have also specified a .vel restart file!
temperature $temperature #跟溫度控制沒毛線關系，只是用來替代vel，告訴系統剛開始原子的速度是多少
outputname $outputname ;#輸出的文件都是以這個開頭
# Periodic Boundary conditions
# NOTE: Do not set the periodic cell basis if you have also
# specified an .xsc restart file!
if {1} {
cellBasisVector1 311.0 0 0 ;#單元基向量
cellBasisVector2 0 364.0 0
cellBasisVector3 0 0 150.0
cellOrigin 144.5627136230 171.1880187988 76.0607299804
}
wrapAll on
#PME (for full-system periodic electrostatics)
if {1} {
PME yes
PMEGridSpacing 1.0
#manual grid definition
PMEGridSizeX 312
PMEGridSizeY 365
PMEGridSizeZ 152 ；#這三個數需要比周期性稍大一點，且能被2、3、5整除（最小公倍數）
}
# Force-Field Parameters
exclude scaled1-4 ;#說明哪一種原子-原子相互作用可以忽略
1-4scaling 0.833333 ;#說明弱化的程度，取值為0-1
scnb 2
cutoff 10.0
switching off ;#設定是否使用過度函數……見下圖
switchdist 10.0
pairlistdist 13.5
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps ;#設定所有與氫相連的鍵為剛性的不震動的。用了rigidbonds，就把與氫原子相連的化學鍵的鍵長固定在平衡值附近了，因為timestep的選取是和體系的振動頻率有關，而氫的振動頻率最快，因此，加上rigidbond就降低了振動頻率，所以才能用2fs，如果不用rigidbond，則2fs的步長太大，用0.5fs比較合適。例外，在溶液中模擬一般用2fs，在真空中一般用0.5fs，也就是不用rigidbond。
rigidTolerance 0.00001
nonbondedFreq 1 ;#設定隔多長時間計算一次總體靜電相互作用
fullElectFrequency 2
stepspercycle 20
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen no ;# don't couple langevin bath to hydrogens
# Constant Pressure Control (variable volume)
if {0} {
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell yes ;# no for water box, yes for membrane
useConstantArea yes ;# no for water box, yes for membrane
####上面的是設置系統壓力的類型，下面的是設置控壓方法，壓力應該有，控壓方法不一定有（只有平衡時才用控壓）。。。溫度設置也是一樣的（）
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.0
langevinPistonDecay 50.0
langevinPistonTemp $temperature
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 500
xstFreq 500
outputEnergies 100
outputPressure 100
# Fixed Atoms Constraint (set PDB beta-column to 1)
#if {0} {
#fixedAtoms on
#fixedAtomsFile myfixedatoms.pdb
#fixedAtomsCol B
#}
# IMD Settings (can view sim in VMD)
#if {0} {
#IMDon on
#IMDport 3000 ;# port number (enter it in VMD)
#IMDfreq 1 ;# send every 1 frame
#IMDwait no ;# wait for VMD to connect before running?
#}
附加參數：
執行腳本：
# prodion
#if {0} {
#minimize 100
#reinitvels $temperature
#}
minimize 1000 ;# 100ps
################################################################################################
Heating’configuration file:
可調參數：
amber on
parmfile ../../complex_0.1.prmtop
ambercoor ../../prod1.rst7
#structure mypsf.psf
#coordinates mypdb.pdb
#outputName myoutput
set temperature 300
outputname ./prod_3
firsttimestep 0
# Continuing a job from the restart files
if {1} { ;#用到上一步的輸出文件
set inputname prod_2
binCoordinates ../$inputname.restart.coor
binVelocities ../$inputname.restart.vel ;# remove the "temperature" entry if you use this!
extendedSystem ../$inputname.restart.xsc
}
模擬參數：
# Input
#paraTypeCharmm on
#parameters par_all27_prot_lipid.inp
# NOTE: Do not set the initial velocity temperature if you
# have also specified a .vel restart file!
#temperature $temperature
# Periodic Boundary conditions
# NOTE: Do not set the periodic cell basis if you have also
# specified an .xsc restart file!
if {0} {
cellBasisVector1 311.0 0 0
cellBasisVector2 0 364.0 0
cellBasisVector3 0 0 150.0
cellOrigin 144.5627136230 171.1880187988 76.0607299804
}
wrapAll on
# Force-Field Parameters
exclude scaled1-4
1-4scaling 0.833333
scnb 2
cutoff 10.0
switching off
switchdist 10.0
pairlistdist 13.5
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
rigidTolerance 0.00001
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20
#PME (for full-system periodic electrostatics)
if {1} {
PME yes
PMEGridSpacing 1.0
#manual grid definition
PMEGridSizeX 312
PMEGridSizeY 365
PMEGridSizeZ 152
}
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen no ;# don't couple langevin bath to hydrogens
# Constant Pressure Control (variable volume)
if {0} {
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell yes ;# no for water box, yes for membrane
useConstantArea yes ;# no for water box, yes for membrane
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.0
langevinPistonDecay 50.0
langevinPistonTemp $temperature
}
restartfreq 1000 ;# 500steps = every 1ps
dcdfreq 3000
xstFreq 3000
outputEnergies 100
outputPressure 100
# Fixed Atoms Constraint (set PDB beta-column to 1)
#if {0} {
#fixedAtoms on
#fixedAtomsFile myfixedatoms.pdb
#fixedAtomsCol B
#}
# IMD Settings (can view sim in VMD)
#if {0} {
#IMDon on
#IMDport 3000 ;# port number (enter it in VMD)
#IMDfreq 1 ;# send every 1 frame
#IMDwait no ;# wait for VMD to connect before running?
#}
附加參數：
reassignFreq 100
reassignTemp 0
reassignIncr 0.1
reassignHold 310 #每隔100步升高0.1k，最終升到310k
執行腳本：
# prodion
#if {0} {
#minimize 100
reinitvels $temperature
#}
#minimize 1000 ;# 100ps
Run 310000
run 1000000
knowledge
1、namd壓力控制
壓力控制需要周期性邊界條件，通過調整unit cell的尺寸和所有原子的坐標（除了固定原子）控制壓力。
壓力的單位為bar。PRESSURE是根據單個原子計算的壓力，GPRESSURE是將氫原子合并到他們相連的重原子上。TEMPAVG、PRESSAVG、GPRESSAVG是之前輸出能量的平均值。第一步中，他們是與TEMP、PRESSURE、GPRESSURE相同的。
總結
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