From: Namd Namd (namd_10_at_yahoo.com)
Date: Thu Jun 28 2012 - 07:25:22 CDT
Dear Norman Geist ,
Thanks for the reply. I used 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
________________________________
Kimden: Norman Geist <norman.geist_at_uni-greifswald.de>
Kime: 'Namd Namd' <namd_10_at_yahoo.com>
Kopya: Namd Mailing List <namd-l_at_ks.uiuc.edu>
Gönderildiği Tarih: 28 Haziran 2012 14:10 Perşembe
Konu: AW: namd-l: wrap dcd files
Hi
First of all the wrapping of coordinates doesn’t effect
velocities and forces if you have used periodic boundary condition. You will
also not need the dcd trajectory to continue a simulation, only the end
coordinates of your previous run.
If you want to continue a simulation with namd, you would just
use the final coor or restart.coor and the corresponding velocities. If you
want to continue with a different md code, you need to know if that code can
read the files that namd produced or how you would need to translate the files.
If the file format is not equal, it’s IMHO not a good idea to translate
velocitiy files as there are to many error sources , like units for example. But
it should be easy to just use the final coordinates and start a new simulation
with another md code and create new velocities there.
Pls. describe what you exactly want to do if that answer doesn’t
help you.
Norman
Von:owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Namd
Namd
Gesendet: Donnerstag, 28. Juni 2012 12:03
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: wrap dcd files
Dear All,
I run md simulations for
trajectory analysis. Should I wrap the dcd ( coordinates ) , velocity dcd and
force dcd files to do trajectory analysis or to continue md simulations with a different md simulation software ? I
think that coord, velocity and force values will change when I wrap the system
using VMD ? Could you give me the information about this issue ?
Thanks for the help.
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