RE: PMEGridSizeX (number of grid points) is very small.

From: Bennion, Brian (Bennion1_at_llnl.gov)
Date: Wed Feb 05 2014 - 12:28:37 CST

maybe no pme grid sizes are given in your conf file?
It is turned on but no dimensions are given for x y or z axes.

Brian

________________________________
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of Rawan Al Nsour [alnsourra_at_vcu.edu]
Sent: Wednesday, February 05, 2014 10:00 AM
To: namd-l
Subject: namd-l: PMEGridSizeX (number of grid points) is very small.

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<mailto:alnsourra_at_vcu.edu>
401 W. Main Street, Room E3216
P.O. Box 843015
Richmond, Virginia 23284-3015

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