https://chemrxiv.org/articles/SMILES_Pair_Encoding_A_Data-Driven_Substructure_Tokenization_Algorithm_for_Deep_Learning/12339368?fbclid=IwAR1np44cDBp20v3PlfkNZzT-LjQrAvRkWBl0ZieSsuBRpA87emg1w3EdOlo
https://github.com/XinhaoLi74/SmilesPE
2020年5月29日 星期五
2020年5月19日 星期二
2020年5月16日 星期六
2020年5月14日 星期四
2020年5月6日 星期三
2020年5月5日 星期二
NAMD-note
Namd2-gpu +p20 conf > log
charm_run ++nodelist nodelist namd_2 +p80 ++ppn 20 prod8.conf > prod8.log &
Minimize’Configuration file：
可调参数：
amber on
parmfile ../complex_0.1.prmtop
ambercoor ../prod1.rst7
#structure mypsf.psf
#coordinates mypdb.pdb
#outputName myoutput
set temperature 300 ;#结构优化时设置没用，但是得有个
set outputname ./prod_2
firsttimestep 0
# Continuing a job from the restart files
if {0} { ;#最小化用不到输入文件，所以设置为不启用
set inputname proding_2
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel ;# remove the "temperature" entry if you use this!
extendedSystem $inputname.xsc
}
模拟参数：
# 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 #跟温度控制没毛线关系，只是用来替代vel，告诉系统刚开始原子的速度是多少
outputname $outputname ;#输出的文件都是以这个开头
# 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 ;#单元基向量
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 ；#这三个数需要比周期性稍大一点，且能被2、3、5整除（最小公倍数）
}
# Force-Field Parameters
exclude scaled1-4 ;#说明哪一种原子-原子相互作用可以忽略
1-4scaling 0.833333 ;#说明弱化的程度，取值为0-1
scnb 2
cutoff 10.0
switching off ;#设定是否使用过度函数……见下图
switchdist 10.0
pairlistdist 13.5
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps ;#设定所有与氢相连的键为刚性的不震动的
rigidTolerance 0.00001
nonbondedFreq 1 ;#设定隔多长时间计算一次总体静电相互作用
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
####上面的是设置系统压力的类型，下面的是设置控压方法，压力应该有，控压方法不一定有（只有平衡时才用控压）。。。温度设置也是一样的（）
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?
#}
附加参数：
执行脚本：
# prodion
#if {0} {
#minimize 100
#reinitvels $temperature
#}
minimize 1000 ;# 100ps
################################################################################################
Heating’configuration file:
可调参数：
amber on
parmfile ../../complex_0.1.prmtop
ambercoor ../../prod1.rst7
#structure mypsf.psf
#coordinates mypdb.pdb
#outputName myoutput
set temperature 300
outputname ./prod_3
firsttimestep 0
# Continuing a job from the restart files
if {1} { ;#用到上一步的输出文件
set inputname prod_2
binCoordinates ../$inputname.restart.coor
binVelocities ../$inputname.restart.vel ;# remove the "temperature" entry if you use this!
extendedSystem ../$inputname.restart.xsc
}
模拟参数：
# 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?
#}
附加参数：
reassignFreq 100
reassignTemp 0
reassignIncr 0.1
reassignHold 310 #每隔100步升高0.1k，最终升到310k
执行脚本：
# prodion
#if {0} {
#minimize 100
reinitvels $temperature
#}
#minimize 1000 ;# 100ps
Run 310000
run 1000000
knowledge
1、namd压力控制
压力控制需要周期性边界条件，通过调整unit cell的尺寸和所有原子的坐标（除了固定原子）控制压力。
压力的单位为bar。PRESSURE是根据单个原子计算的压力，GPRESSURE是将氢原子合并到他们相连的重原子上。TEMPAVG、PRESSAVG、GPRESSAVG是之前输出能量的平均值。第一步中，他们是与TEMP、PRESSURE、GPRESSURE相同的。
參考
https://my.oschina.net/u/4373914/blog/3466746
訂閱：
文章 (Atom)