From: Greg Guthe (gguthe_at_gmail.com)
Date: Thu May 21 2009 - 15:32:47 CDT
Hi,
Does PME require periodic boundaries for all three dimensions? I'd
like a periodic boundary and PME for just one, but NAMD throws "PME
requires periodic boundary conditions." Is the only solution to make a
wide periodic box or am I implementing something wrong?
Thanks,
Greg
Related: http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/7876.html
I'm using this config file:
# Input Parameters
amber yes
ambercoor doesitexplode.rst7
parmfile doesitexplode.parm7
# Output Parameters
outputname ./doesitexplode
binaryoutput yes
restartfreq 1000
DCDfreq 100
# Timestep Parameters
numsteps 10000
timestep 1.0 # (fs)
# Simulation Space Partitioning Parameters
cutoff 12
switching on
switchdist 10
pairlistdist 14.5
splitpatch hydrogen
# Basic Dynamics Parameters
exclude none
temperature 300 # (K) room temp 20C
# Periodic Box Boundaries
cellBasisVector1 0 0 25
cellOrigin 0 0 0
#wrapAll on
# Particle Mesh Ewald (PME)
PME yes
PMEGridSpacing 1.0
#PMEGridSizeZ 2
fullElectFrequency 5
# Cylindrical Harmonic Boundary Conditions
#cylindricalBC on
#cylindricalBCCenter 0 0 10
#cylindricalBCr1 50
#cylindricalBCl1 1500 # i.e. long
#cylindricalBCk1 50
# Fixed Atom Parameters
#fixedAtoms yes
#fixedAtomsFile fixedfixed.pdb
# Langevin Dynamics Parameters
#langevin yes
#langevintemp 300
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