From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Jul 02 2012 - 09:00:43 CDT
On Mon, Jul 2, 2012 at 3:30 PM, Namd Namd <namd_10_at_yahoo.com> wrote:
> 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
there is no point in wrapping velocities and forces. how would that work at all?
> analysis ? or Can I use coordinates, velocities and forces witout wrapping
> for trajectory analysis ? Also Are wrapped velocities and forces values
whether you need wrapped or unwrapped coordinates or whether it doesn't
matter, depends very much on the kind of analysis that you want to do.
it is usually easier/faster to wrap an unwrapped trajectory, but you may
loose a bit or two in accuracy and visualization may not be as nice right
out of the box. similarly, it is possible to unwrap a trajectory after the fact.
> different from the unwrapped velocities and forces values ? Could you give
> me the information about this issue ?
i suggest you make some experiments on a tiny test system and
find the best approach that fits your needs best. no point in deciding
either way, when you don't know what you need and what you can
work with the best.
axel.
>
> 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
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy.
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