From: Rawan Al Nsour (alnsourra_at_vcu.edu)
Date: Wed Feb 05 2014 - 12:00:57 CST
Dear All,
I ran a simulation for small molecular C4F10 and it is failed, what is the
solution in this case?
below is the conf file
structure ptfe.psf
coordinates ptfe.pdb
outputName nvt-01
set temperature 280
firsttimestep 0
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 2.7 0.0 0.0
cellBasisVector2 0.0 5.06 0.0
cellBasisVector3 0.0 0.0 2.7
cellOrigin 0.0 0.0 0.0
}
wrapAll on
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 7.0
switching on
switchdist 5.0
pairlistdist 8.5
# 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 50 ;# 500steps = every 1ps
dcdfreq 25
xstFreq 25
outputEnergies 10
outputPressure 10
minimize 50
run 250 ;# 0.1 ns
Thanks,
-- 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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