Re: cell size

From: Hasan haska (hasanhaska_at_yahoo.com)
Date: Wed Dec 14 2011 - 06:41:10 CST

Dear Axel, Thanks for your help. I used “pbc wrap –all” command in VMD and got  the coordinates of all water molecules in defined cell sizes ( 40 40 65 ). Then again I used these coordinates to run another md to see if I can transfer wrapped molecule coordinates into another md system and continue md simulation.  But, when I run md which starts with a short minimization with wrapped water molecule coordinates I saw the error in below. How can I solve this problem?   I want to run md simulations for Liquid/Liquid Interfaces.  So First I should equilibrate the water  molecules and combinewater molecules with a different type of equilibrated molecules to genetate a Liquid/Liquid Interface system then run md for the Liquid/Liquid Interface system. I especially searched for some tutorials or sources for generating Liquid/Liquid Interface system with NAMD and VMD but I coludn’t find anything. Could you please help me about generating the interface system ?     TCL: Minimizing for 1000 steps Warning: Low global exclusion count, possible error! Warning: This warning is not unusual during minimization. Warning: Increasing pairlistdist or cutoff may avoid this. PRESSURE: 0 -4418.82 -2.05598 156.051 -2.05598 -4901.6 42486.6 156.051 42486.6 -5.53326e+07 GPRESSURE: 0 -6732.9 704.952 287.812 -1872.49 -5514.03 40747.7 -22321.4 23202.3 -5.33443e+07 ETITLE:      TS           BOND          ANGLE          DIHED          IMPRP               ELECT            VDW       BOUNDARY           MISC        KINETIC               TOTAL           TEMP      POTENTIAL         TOTAL3        TEMPAVG            PRESSURE      GPRESSURE         VOLUME       PRESSAVG      GPRESSAVG   ENERGY:       0 125379181.5818      4446.9155         0.0000         0.0000         -49473.7045      8194.2763         0.0000         0.0000         0.0000      125342349.0692         0.0000 125342349.0692 125342349.0692         0.0000      -18447311.4967 -17785523.1787    320000.0000 -18447311.4967 -17785523.1787   OPENING EXTENDED SYSTEM TRAJECTORY FILE MINIMIZER SLOWLY MOVING 115 ATOMS WITH BAD CONTACTS DOWNHILL Warning: Low global exclusion count, possible error! Warning: This warning is not unusual during minimization. Warning: Increasing pairlistdist or cutoff may avoid this. PRESSURE: 1 -4374.24 -3.04685 157.66 -3.04685 -4855.75 42482.4 157.66 42482.4 -5.53325e+07 GPRESSURE: 1 -6676.79 671.979 302.936 -1858.45 -5466.59 40737.3 -22320.5 23195 -5.33442e+07 ENERGY:       1 125379181.5818      4446.9155         0.0000         0.0000         -49550.7012      8257.6139         0.0000         0.0000         0.0000      125342335.4100         0.0000 125342335.4100 125342335.4100         0.0000      -18447252.8218 -17785457.4470    320000.0000 -18447252.8218 -17785457.4470   ...   ________________________________ From: Axel Kohlmeyer <akohlmey_at_gmail.com> To: Hasan haska <hasanhaska_at_yahoo.com> Cc: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu> Sent: Tuesday, December 13, 2011 6:00 PM Subject: Re: namd-l: cell size On Tue, Dec 13, 2011 at 10:47 AM, Hasan haska <hasanhaska_at_yahoo.com> wrote: > > ________________________________ > From: Hasan haska <hasanhaska_at_yahoo.com> > To: Axel Kohlmeyer <akohlmey_at_gmail.com> > Sent: Tuesday, December 13, 2011 5:46 PM > > Subject: Re: namd-l: cell size > > Dear Axel, > > I modified the conf file like in below and run a short md but I still got > the some water molecules' coordinates outside the box. I think this is > normal since I use PBC. Is there any other way to get the coordinates in a > periodic box ( 40 40 65 ) ? have you tried using wrapAll ? http://www.ks.uiuc.edu/Research/namd/2.8/ug/node33.html other than that, wrapping of coordinates can easily done in post-processing, e.g. using the pbctools plugin in VMD. axel. > > Thanks for your help. > > useGroupPressure   no > useFlexibleCell       no > useConstantArea    no > > ________________________________ > From: Axel Kohlmeyer <akohlmey_at_gmail.com> > To: Hasan haska <hasanhaska_at_yahoo.com> > Cc: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu> > Sent: Tuesday, December 13, 2011 4:21 PM > Subject: Re: namd-l: cell size > > On Tue, Dec 13, 2011 at 9:10 AM, Hasan haska <hasanhaska_at_yahoo.com> wrote: >> 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 ? > > don't use a flexible cell? > > axel. > >> >> 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 >> >> ************* > > > > -- > Dr. Axel Kohlmeyer > akohlmey_at_gmail.com  http://goo.gl/1wk0 > > College of Science and Technology > Temple University, Philadelphia PA, USA. > > > > -- Dr. Axel Kohlmeyer akohlmey_at_gmail.com  http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA.

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:03 CST