From: Hasan haska (hasanhaska_at_yahoo.com)
Date: Tue Mar 10 2015 - 16:51:30 CDT
DearNAMD users,
Iwant to minimize and equilibrate a bulk water system that includes 7048water molecules (SPC/E water model) in a rectangular box with the d=0.996 g/cm3experimental density at 300K. Therefore I prepared a namd conf file belowand started to run it. But after minimization was completed I got the error,which is in below. My aim is to run minimization and NPT simulation withkeeping the dimension of the unit cell in the x-y plane constant while allowingfluctuations along the z axis in order to get the real cell sizes ( 55 X 55 X70 Angs ) according to the density. Then run a NVT simulation with these cellsize. How can I solve this problem ? Could you please share your opinionand experience ?
Thanks.
http://www.filedropper.com/water_1
My simulation files are in the linkabove.
*****************************
Error:
------------- Processor 0 Exiting:Called CmiAbort ------------
Reason: FATAL ERROR: Stray PME gridcharges detected!
FATAL ERROR: Seehttp://www.ks.uiuc.edu/Research/namd/bugreport.html
Charm++ fatal error:
FATAL ERROR: Stray PME grid chargesdetected!
**************************
#--- This is a test namd configurationfile
#############################################################
##
#############################################################
paratypeCharmm on
parameters water.PRM
structure water.psf #
coordinates water_.pdb #
outputName water_1out #
set temperature 300
temperature $temperature
firsttimestep 0
# Integrator Parameters
timestep 1.0
nonbondedFreq 2
fullElectFrequency 4
stepspercycle 16
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 18.
switching on
switchdist 15.
pairlistdist 20.
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen on ;# couple langevin bath to hydrogens
# Constant Pressure Control (variablevolume)
useGroupPressure no ;# 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
#--- PBC
cellBasisVector1 55.0 0.0 0.0
cellBasisVector2 0.0 55.0 0.0
cellBasisVector3 0.0 0.0 100.0
#--- PME
PME yes
PMEGridSpacing 1.0
#--- Output & Restart
binaryoutput no
binaryrestart yes
restartname water_1restart #
DCDfile water_1out.dcd #
restartfreq 5000 #
dcdfreq 5000
xstFreq 5000
outputEnergies 5000
outputPressure 5000
outputtiming 5000
minimize 10000
reinitvels $temperature
run 10000000
# 10 ns 2002 record
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