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金虫 (小有名气)

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专业: 无机化工

[求助] 用NAMD进行NEMD过程遇到问题，加力不均匀

我用NAMD进行NEMD模拟，用石墨烯片对水盒子施加压力（z方向是加力方向），但在进行的过程中石墨烯片会出现倾斜（图1）或者旋转（图2），这样加力就不均匀了，请问各位大神是否知道是什么原因，或者是哪里设置的问题？我的体系是两个水盒子之间夹了一个CNT的反渗透模型，然后用两个石墨烯片放在两头对水盒子施加压力。
下面是我的.conf文件
set sysname watbox-grap-1

structure       ./${sysname}.psf
coordinates       ./${sysname}.pdb

set temperature 300
set outputname    ./NEMD1/${sysname}

# Continuing a job from the restart files
if {0} {
set inputname    ./03-output/run
binCoordinates    $inputname.restart.coor
binVelocities    $inputname.restart.vel  ;# remove the "temperature" entry if you use this!
extendedSystem    $inputname.restart.xsc
}

firsttimestep    0

#############################################################
## SIMULATION PARAMETERS                                  ##
#############################################################

# Input
paraTypeCharmm       on
parameters       ./par_pa.prm

# NOTE: Do not set the initial velocity temperature if you
# have also specified a .vel restart file!
  temperature       $temperature

# Periodic Boundary conditions
if {1} {
cellBasisVector1 45.0    0. 0.
cellBasisVector2    0.    45.0 0.
cellBasisVector3    0.    0. 258.0
cellOrigin       0.    0. 0.
}
wrapAll          on
margin             10.0

# Force-Field Parameters
exclude          scaled1-4
1-4scaling       1.0
cutoff             12.
switching          on
switchdist       10.
pairlistdist       14.5

# Integrator Parameters
timestep          1 ;# 1fs/step

rigidBonds       all
rigidTolerance    10e-8
rigidIterations    100

nonbondedFreq    1
fullElectFrequency  2
stepspercycle    20

#PME (for full-system periodic electrostatics)
if {1} {
PME                yes
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    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  200.
langevinPistonDecay 50.
langevinPistonTemp $temperature
}

# Output
outputName       $outputname
restartfreq       1000    ;# 1000steps = every 1ps
dcdfreq          1000
xstFreq          1000
outputEnergies    1000
outputPressure    1000

# Fixed Atoms Constraint (set PDB beta-column to 1) ； #固定CNT
if {1} {
fixedAtoms       on
fixedAtomsFile    fixatoms-1.pdb
fixedAtomsCol    B
fixedAtomsForces on
}

#############################################################
## EXTRA PARAMETERS                                     ##
#############################################################

# Put here any custom parameters that are specific to
# this job (e.g., SMD, TclForces, etc...)
if {1} {
tclforces          on
set waterCheckFreq 100
set allatompdb       ${sysname}.pdb
tclForcesScript    addforce.tcl
}

#############################################################
## EXECUTION SCRIPT                                     ##
#############################################################
# Minimization
if {1} {
minimize          1000
reinitvels       $temperature
}

run 2000000 ;# 2.0 ns

图1.png