AW: wrap dcd files

From: Namd Namd (
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 <> Kime: 'Namd Namd' <> Kopya: Namd Mailing List <> 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 [] Im Auftrag von Namd Namd Gesendet: Donnerstag, 28. Juni 2012 12:03 An: 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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