From: Namd Namd (namd_10_at_yahoo.com)
Date: Mon Jul 02 2012 - 08:30:17 CDT
Dear All,
I use periodic boundary conditions in my namd simulations. And I generated coord.dcd, vel.dcd and force.dcd files. The conf file is in below. Should I use the wrapped coordinates, velocities and forces when I do trajectory analysis ? or Can I use coordinates, velocities and forces witout wrapping for trajectory analysis ? Also Are wrapped velocities and forces values different from the unwrapped velocities and forces values ? Could you give me the information about this issue ?
Kind regards.
paratypeCharmm on
parameters x.prm
structure x.psf
coordinates x.pdb
outputName x_7out
set temperature 309
# temperature $temperature
# continuing a run
set inputname x_6restart
binCoordinates $inputname.coor
binVelocities $inputname.vel
extendedSystem $inputname.xsc
firsttimestep 43770000
# Integrator Parameters
timestep 2
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
rigidBonds all
# Force-Field Parameters
exclude scaled1-4
1-4scaling 0.8333333
cutoff 12
switching on
switchdist 9
pairlistdist 14
# Constant Temperature Control nvt
langevin on
langevinDamping 5
langevinTemp $temperature
langevinHydrogen off
#--- PBC
cellBasisVector1 47.036 0.0 0.0
cellBasisVector2 0.0 47.036 0.0
cellBasisVector3 0.0 0.0 300.0
#--- PME
dielectric 1
PME on
PMEGridSizeX 48
PMEGridSizeY 48
PMEGridSizeZ 300
#--- Output & Restart
binaryoutput no
binaryrestart yes
restartname x_7restart
DCDfile x_7out.dcd
velDCDfile x_7out.vel.dcd
restartfreq 1000
dcdfreq 1000
xstFreq 1000
outputEnergies 1000
forceDCDfreq 1000
velDCDfreq 1000
outputPressure 1000
outputtiming 1000
run 5000000
# 10 ns 5000 record
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