about dcd files

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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