From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Mar 11 2015 - 02:03:46 CDT
>From the Error message one can conclude instability of your system. The error message points out, that the grid charges for PME have changed more than expected between timesteps, which results from really fast atoms. The most likely reason are bad contacts in the initial structure and too short minimization. So increase the number of minimization steps to approx. 10000 steps. Also check the TOTAL energy of the system for convergence during the minimization run (VMDs Namd Plot plugin is useful for that).
For the latter NPT run, you are interested in:
useflexiblecell yes
useconstantarea yes
along with the piston pressure to have only Z changing.
Norman Geist.
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of Hasan haska
Sent: Tuesday, March 10, 2015 10:52 PM
To: NAMD List
Subject: namd-l: equilibrate the bulk water system
Dear NAMD users,
I want to minimize and equilibrate a bulk water system that includes 7048 water molecules (SPC/E water model) in a rectangular box with the d=0.996 g/cm3 experimental density at 300K. Therefore I prepared a namd conf file below and 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 with keeping the dimension of the unit cell in the x-y plane constant while allowing fluctuations along the z axis in order to get the real cell sizes ( 55 X 55 X 70 Angs ) according to the density. Then run a NVT simulation with these cell size. How can I solve this problem ? Could you please share your opinion and experience ?
Thanks.
http://www.filedropper.com/water_1
My simulation files are in the link above.
*****************************
Error:
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Stray PME grid charges detected!
FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
Charm++ fatal error:
FATAL ERROR: Stray PME grid charges detected!
**************************
#--- This is a test namd configuration file
#############################################################
##
#############################################################
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 (variable volume)
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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