cell size

From: Hasan haska (hasanhaska_at_yahoo.com)
Date: Tue Dec 13 2011 - 08:10:49 CST

Dear Namd Users,   I run 5 ns md simulation for water molecules with the conf file below. And I want to get the final coordinates of all water molecules in defined cell sizes ( 40 40 65 ) . How can I do this operation in NAMD ?   Thank you very much for your help.   Regards.   ********* #--- This is a test namd configuration file paratypeCharmm  on parameters    water.prm structure              water.psf coordinates            water.pdb outputName             water_1out set temperature    300 temperature $temperature firsttimestep      0 # Integrator Parameters timestep            1 nonbondedFreq       1 fullElectFrequency  5 stepspercycle       10 # Force-Field Parameters exclude        scaled1-4 1-4scaling    0.8333333 cutoff          19.7 switching       on switchdist      17  pairlistdist    24 # Constant Temperature Control langevin            on    ;# do langevin dynamics langevinDamping     5     ;# damping coefficient (gamma) of 5/ps langevinTemp        $temperature langevinHydrogen    on    ;# don't couple langevin bath to hydrogens #--- PBC cellBasisVector1  40. 0.0  0.0 cellBasisVector2  0.0  40.  0.0 cellBasisVector3  0.0  0.0  65. #--- PME dielectric      1 PME             on PMEGridSizeX    45 PMEGridSizeY    45 PMEGridSizeZ    72 # Constant Preswaterre Control (variable volume) useGroupPressure   no useFlexibleCell       yes  useConstantArea       yes  langevinPiston        on langevinPistonTarget  1.01325 ;#  in bar -> 1 atm langevinPistonPeriod  200. langevinPistonDecay   100. langevinPistonTemp    $temperature #--- Output & Restart binaryoutput    no binaryrestart   yes restartname     water_restart DCDfile         water_out.dcd restartfreq        1250 dcdfreq            1250 xstFreq            1250 outputEnergies     1250 forceDCDfreq       1250 outputPressure     1250 outputtiming       1250 minimize 12500 reinitvels          $temperature run 5000000 *************

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