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kevin8871

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[交流] 【求助】用NAMD 做NPT模拟遇到下面的问题

本人用NAMD做NPT模拟，遇到了下面的问题
FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
这是为什么？下面是我的conf file
structure       3HT_20.psf
coordinates    3HT_20_centered.pdb

set outputname    NPT file for 3 HT

#continuing a run
set inputname    nimi
binVelocities    3HT_20_mini.restart.vel
bincoordinates    3HT_20_mini.restart.coor
extendedsystem    3HT_20_mini.restart.xsc
firsttimestep    6000
numsteps          2506000

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

# Input

paraTypeCharmm       on
parameters          ht_monomer.par
# Force-Field Parameters
exclude          scaled1-4
1-4scaling       1.0
cutoff             12.
switching          on
switchdist       10.
pairlistdist       13.5

# Integrator Parameters
timestep          2.0  ;# 2fs/step
rigidBonds       all  ;# needed for 2fs steps
nonbondedFreq    1
fullElectFrequency  2
stepspercycle    10

# Constant Temperature Control
langevin          on ;# do langevin dynamics
langevinDamping    5    ;# damping coefficient (gamma) of 5/ps
langevinTemp       300
langevinHydrogen off ;# don't couple langevin bath to hydrogens

#PBC
wrapall    on
cellBasisVector1 31.312999725341797 0.0 0.0
cellBasisVector2    0.0 32.558000564575195 0.0
cellBasisVector3    0.0 0 45.066001892089844
cellOrigin       -3.0093722216406604e-6 1.4230939996195957e-5 2.136936927854549e-6

wrapAll          on

# PME (for full-system periodic electrostatics)
PME                yes
PMEGridSizeX       42
PMEGridSizeY       43
PMEGridSizeZ       55

# Constant Pressure Control (variable volume)
useGroupPressure    yes ;# needed for rigidBonds
useFlexibleCell    no  ;# no for water box yes for membrane
useConstantArea    no  ;# no for waterbox, maybe for membrane

langevinPiston       on
langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
langevinPistonPeriod  100.
langevinPistonDecay 50.
langevinPistonTemp 300

# Output
outputName       $outputname

restartfreq       2500    ;# 2500steps = every 5ps
dcdfreq          1000    ;# 1000steps = every 2ps
xstFreq          1000
outputEnergies    500
outputPressure    500

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

#############################################################
## EXECUTION SCRIPT                                     ##
#############################################################

# Minimization

run 2500000 ;# 5ns

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