From: shreya bhattacharya (shreya199713_at_gmail.com)
Date: Fri Sep 09 2022 - 00:30:15 CDT
Hi everyone,
I was having no problem in running normal simulation in my system. My
system has only 55k atoms. But, as soon as I start the equilibration of FEP
simulation, I am getting the following error:
FATAL ERROR: CudaTileListKernel::buildTileLists, maximum shared memory
allocation exceeded. Too many atoms in a patch
The configuration file is as follows:
#############################################################
## JOB DESCRIPTION ##
#############################################################
# equil before fep
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
margin 1
structure ../E2V.psf
coordinates ../E2V.pdb
set temperature 310
set outputname equil
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
mergeCrossterms yes
parameters ../toppar/par_all36_prot.prm
parameters ../toppar/par_all36_na.prm
parameters ../toppar/par_all36_carb.prm
parameters ../toppar/par_all36_lipid.prm
parameters ../toppar/par_all36_cgenff.prm
parameters ../toppar/toppar_all36_prot_arg0.str
parameters ../toppar/toppar_all36_prot_na_combined.str
parameters ../toppar/toppar_all36_prot_model.str
parameters ../toppar/toppar_all36_prot_modify_res.str
parameters ../toppar/toppar_all36_na_nad_ppi.str
parameters ../toppar/toppar_all36_na_rna_modified.str
parameters ../toppar/toppar_water_ions_namd.str
parameters ../toppar/toppar_all36_moreions.str
temperature $temperature
# Force-Field Parameters
# These are specified by CHARMM
exclude scaled1-4
1-4scaling 1.0
switching on
# You have some freedom choosing the cutoff
cutoff 12. ;# may use smaller, maybe 10., with PME
switchdist 11. ;# cutoff - 1. here
# Promise that atom won't move more than 2A in a cycle
#pairlistdist 14. ;# cutoff + 2.
#stepspercycle 10 ;# redo pairlists every ten steps
# Integrator Parameters
timestep 2.0 ;# 2fs/step
nonbondedFreq 1 ;# nonbonded forces every step
fullElectFrequency 2 ;# PME only every other step
#Harmonic restraint parameters
rigidBonds all
rigidTolerance 1.0e-8
rigiditerations 400
# Periodic Boundary Conditions
cellBasisVector1 84.91 0 0
cellBasisVector2 0 84.81700000000001 0
cellBasisVector3 0 0 85.101
cellOrigin -0.2270000000000003 -0.1504999999999974 0.14450000000000074
wrapWater on ;# wrap water to central cell
wrapAll on ;# wrap other molecules too
wrapNearest off ;# use for non-rectangular cells
# full electrostatics
# PME (for full-system periodic electrostatics)
PME yes
# let NAMD determine grid
PMEGridSpacing 1.0
# Constant Temperature Control
langevin on ;#do langevin dynamics
langevinDamping 5 ;#damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigid bonds
useFlexibleCell no ;# no for water box, yes for membrane
useConstantArea no ;# no for water box, maybe for membrane
langevinPiston on
langevinPistonTarget 1.01325 ;# pressure in bar -> 1 atm
langevinPistonPeriod 200. ;# oscillation period around 200 fs
langevinPistonDecay 100. ;# oscillation decay time of 100 fs
langevinPistonTemp $temperature ;# coupled to heat bath
StrainRate 0.0 0.0 0.0
# COM
ComMotion no
#output files
binaryoutput no
binaryrestart no
outputName $outputname ;# base name for output from this run
restartfreq 5000 ;# 5000 steps = every 10ps
dcdfreq 5000
xstFreq 5000
outputEnergies 1000
outputTiming 5000 ;# shows time per step and time to
completion
#############################################################
## EXTRA PARAMETERS ##
#############################################################
CUDASOAintegrate off
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# FEP PARAMETERS
# FEP PARAMETERS
source ../../tools/fep.tcl
alch on
alchType FEP
alchFile ../E2V.fep
alchCol B
alchOutFile aqua-equil.fepout
alchOutFreq 1000
alchVdwLambdaEnd 1.0
alchElecLambdaStart 0.5
alchVdWShiftCoeff 4.0
alchDecouple off
alchEquilSteps 10000
set numSteps 50000
set numMinSteps 5000
runFEPmin 0.0 0.0 0.0 $numSteps $numMinSteps $temperature
Kindly help me with this
-- *Regards,* *Shreya Bhattacharya*
This archive was generated by hypermail 2.1.6 : Tue Dec 13 2022 - 14:32:44 CST