From: Rawan Al Nsour (alnsourra_at_vcu.edu)
Date: Thu May 15 2014 - 11:19:21 CDT
Dear All,
I am working on a polymer layer, I started with nvt and I got the following
errors at the first timestep. As you may see from the conf file below I
decrease the cutoff less than the perodic cell in the y direction (i.e.
y=7.3 A). what other solutions do you recommend?
Warning: High global exclusion count, possible error!
Warning: This warning is not unusual during minimization.
Warning: Decreasing pairlistdist or cutoff that is too close to periodic
cell size may avoid this.
PRESSURE: 0 2.95017e+07 3.58273e+06 1.43404e+08 3.58273e+06 6.55761e+07
7.74877e+07 1.43404e+08 7.74877e+07 8.83632e+09
GPRESSURE: 0 2.95017e+07 3.58273e+06 1.43404e+08 3.58273e+06 6.55761e+07
7.74877e+07 1.43404e+08 7.74877e+07 8.83632e+09
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
POTENTIAL TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 0 340.7311 93.0033 -3960.1321
0.0000 -1520.1712 668285651.4547 0.0000
0.0000 0.0000 668280604.8859 0.0000 668280604.8859
668280604.8859 0.0000 2977132396.3186 2977132396.3186
62413.3356 2977132396.3186 2977132396.3186
OPENING EXTENDED SYSTEM TRAJECTORY FILE
MINIMIZER SLOWLY MOVING 976 ATOMS WITH BAD CONTACTS DOWNHILL
FATAL ERROR: Periodic cell has become too small for original patch grid!
FATAL ERROR: Periodic cell has become too small for original patch grid!
FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
.........................................................................................
the configuratio file is like this
structure 196c5.psf
coordinates 196c5.pdb
outputName nvt-01
set temperature 300
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters par_all27_prot_lipid.inp
temperature $temperature
# Periodic Boundary Conditions
# NOTE: Do not set the periodic cell basis if you have also
# specified an .xsc restart file!
if {1} {
cellBasisVector1 92.53 0.0 0.0
cellBasisVector2 0.0 7.30 0.0
cellBasisVector3 0.0 0.0 92.40
cellOrigin 44.78 0.0 44.79
}
wrapAll on
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 5.0
switching on
switchdist 3.0
pairlistdist 6.5
margin 7.5
vdwGeometricSigma yes
# Integrator Parameters
timestep 0.5 ;# 1fs/step
rigidBonds none ;# needed for 1fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20
#PME (for full-system periodic electrostatics)
if {1} {
PME yes
PMEGridSpacing 1.0
}
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
restartfreq 1000 ;# 1000steps = every 2ps
dcdfreq 1000
xstFreq 1000
outputEnergies 100
outputPressure 100
minimize 500
run 100000 ;# 0.5 ns
-- Rawan Al Nsour Ph.D. Candidate Department of Mechanical and Nuclear Engineering School of Engineering, Virginia Commonwealth University E-mail: alnsourra_at_vcu.edu 401 W. Main Street, Room E3216 P.O. Box 843015 Richmond, Virginia 23284-3015
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