From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Thu Jul 14 2022 - 08:39:39 CDT
How big is your simulation box, and how was it made? Usually, the problem is a box that is either too big (unlikely for a 30x30x30 box), too small, or doesn’t have enough atoms in it to maintain something close to the original density.
-Josh
From: <owner-namd-l_at_ks.uiuc.edu> on behalf of Nur Afiqah Ahmad <nur_afiqah.ahmad_at_unsw.edu.au>
Reply-To: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>, Nur Afiqah Ahmad <nur_afiqah.ahmad_at_unsw.edu.au>
Date: Thursday, July 14, 2022 at 9:33 AM
To: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
Subject: namd-l: Error
Hai, I want to do an FEP calculation for methane in octanol solution. However, I’m getting an error while running the equilibration step. Here is the error.
Reason: FATAL ERROR: Periodic cell has become too small for the original patch grid! Possible solutions are to restart from a recent checkpoint, increase margin, or disable useFlexibleCell for liquid simulation.
I’m already trying the solution from the previous list which tries to restart the simulation from the previous checkpoint and by increasing the margin but it doesn't work. Can anyone help me to solve the problem? Attach here also my configuration file.
#############################################################
## JOB DESCRIPTION ##
#############################################################
# Minimize followed by Production Run
structure mixture.psf
coordinates mixture.pdb
set temperature 300 ;# target temperature used several times below
# starting from scratch
temperature $temperature ;# initialize velocities randomly
outputName eq ;# base name for output from this run
restartfreq 5000 ;# 1000 steps = every 1ps
dcdfreq 5000
outputEnergies 5000 ;# 100 steps = every 0.2 ps
outputpressure 5000
XSTFreq 5000
# Force-Field Parameters
paraTypeCharmm on
parameters ../toppar/par_all36_cgenff.prm
parameters ../toppar/par_all36_carb.prm
parameters ../toppar/par_all36_lipid.prm
parameters ../toppar/par_all36_na.prm
parameters ../toppar/par_all36_prot.prm
parameters ../toppar/par_all36m_prot.prm
parameters toppar_methane.str
parameters ../toppar/toppar_water_ions_namd.str
# system dimensions
cellBasisVector1 30.000 0.000 0.000
cellBasisVector2 0.000 30.000 0.000
cellBasisVector3 0.000 0.000 30.000
cellOrigin -0.17385032773017883 -0.10125097632408142 -0.045012082904577255
wrapAll on
wrapWater on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSpacing 1.0
# These are specified by CHARMM
exclude scaled1-4 # non-bonded exclusion policy to use "none,1-2,1-3,1-4,or scaled1-4"
1-4scaling 1.0
switching on
vdwForceSwitching yes; # New option for force-based switching of vdW
cutoff 13.5; # may use smaller, maybe 10., with PME
switchdist 10.0; # cutoff - 2.
pairlistdist 16.0; # stores the all the pairs with in the distance it should be larger
stepspercycle 20; # 20 redo pairlists every ten steps
pairlistsPerCycle 2; # 2 is the default
Margin 4.0;
# CONSTRAINTS
#fixedAtoms on
#fixedAtomsFile freeze.fep
#fixedAtomsCol B
#fixedAtomsForces on
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1 ;# nonbonded forces every step
fullElectFrequency 2 ;# PME only every other step
# Constant Temperature Control
langevin on ;# langevin dynamics
langevinDamping 1.0 ;# damping coefficient of 1/ps
langevinTemp $temperature ;# random noise at this level
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 50.0
langevinPistonDecay 25.0
langevinPistonTemp $temperature
# Colvars can be used to restrain movement of the center of mass
#colvars on
#colvarsConfig fixoctdistance20.in
#############################################################
## EXECUTION SCRIPT ##
#############################################################
minimize 1000
run 5000000 ;# 5ns
exit
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