momoqianxing的个人博客分享 http://blog.sciencenet.cn/u/momoqianxing

博文

NAMD中使用隐式溶剂GBIS进行分子动力学模拟

已有 6084 次阅读 2011-8-18 11:36 |个人分类:分子模拟|系统分类:科研笔记

#############################################################
## JOB DESCRIPTION                                         ##
#############################################################
# Minimization and Equilibration of decrosin
# In a water box.  The mdrun for nvt
#############################################################
## ADJUSTABLE PARAMETERS                                   ##
#############################################################
structure          dec-nos3.psf
coordinates        dec-nos3.pdb
outputName         dec_md1
set temperature    310
# Continuing a job from the restart files
if {1} {
set inputname      dec_heat
binCoordinates     $inputname.restart.coor
binVelocities      $inputname.restart.vel ;# remove the "temperature" entry if you use this!
extendedSystem    $inputname.xsc
}
firsttimestep      0

#############################################################
## SIMULATION PARAMETERS                                   ##
#############################################################
# Param 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
 
#  GBIS parameters
GBIS                 on
ionConcentration     0.1
alphaCutoff          14
solventDielectric    78.5
intrinsicRadiusOffset 0.09
# Periodic Boundary conditions
# NOTE: Do not set the periodic cell basis if you have also
# specified an .xsc restart file!
if {0} {
cellBasisVector1    52.    0.   0.
cellBasisVector2     0.   47.   0.
cellBasisVector3     0.    0   49.
cellOrigin          3.5  -0.5  -1.9
}
wrapWater           on
wrapAll             on

# Force-Field Parameters
exclude             scaled1-4
1-4scaling          1.0
cutoff              16.0
switching           on
switchdist          15.0
pairlistdist        17.5
# margin              5

# Integrator Parameters
timestep            1.0  ;# 1fs/step
rigidBonds          all  ;# needed for 2fs steps
nonbondedFreq       2
fullElectFrequency  4 
stepspercycle       12

#PME (for full-system periodic electrostatics)
if {0} {
PME                 yes
# PMEGridSizeX        80
# PMEGridSizeY        80
# PMEGridSizeZ        60
PMEGridSpacing      1.0
}

# Constant Temperature Control
langevin            on    ;# do langevin dynamics
langevinDamping     5     ;# 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       no  ;# no for water box, yes for membrane
useConstantArea       no  ;# no for water box, yes for membrane
langevinPiston        on
langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
langevinPistonPeriod  100.
langevinPistonDecay   50.
langevinPistonTemp    $temperature
}
 

# Fixed Atoms Constraint (set PDB beta-column to 1)
if {0} {
fixedAtoms          on
fixedAtomsFile      dec-2238_wi.pdb
fixedAtomsCol       B
}
# Harmonic restraint parameters
if {0} {
constraints         on
consexp             2
consref             cfd_wi.cstr
conskfile           cfd_wi.cstr
conskcol            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?
}

# Output Freq.
restartfreq         6000     ;# 1000steps = every 1ps
dcdfreq             6000
xstFreq             6000
outputEnergies      1200
outputPressure      1200
#############################################################
## EXTRA PARAMETERS                                        ##
#############################################################
# Put here any custom parameters that are specific to
# this job (e.g., SMD, TclForces, etc...)
 
#############################################################
## EXECUTION SCRIPT                                        ##
#############################################################

run 60000000 ;# 60ns
pdb,psf,不加水不加离子
# Force-Field Parameters
cutoff              16.0
switchdist          15.0
pairlistdist        17.5
# Integrator Parameters
timestep            1.0  ;# 1fs/step
rigidBonds          all  ;# needed for 2fs steps
nonbondedFreq       2
fullElectFrequency  4 
stepspercycle       12
无PME PBC,NVT进行md
速度大概为含水md的四倍


https://blog.sciencenet.cn/blog-269219-476699.html


下一篇:windows下使用F-Secure SSH Client自动登录linux服务器
收藏 IP: 114.212.200.*| 热度|

0

该博文允许注册用户评论 请点击登录 评论 (1 个评论)

数据加载中...

Archiver|手机版|科学网 ( 京ICP备07017567号-12 )

GMT+8, 2024-6-16 05:11

Powered by ScienceNet.cn

Copyright © 2007- 中国科学报社

返回顶部