Hi Dallas / all I looked up at the pressure coupling section and i found how to keep the box size same for two axis and change only one axis (i used semiisotropic pressure coupling type) but when i did that the average pressure i get after the run is negative where as i want it be close to 1 bar?. i dont know what might have gone wrong.
Energy Average RMSD Fluct. Drift Tot-Drift ------------------------------------------------------------------------------- Pressure (bar) -661.673 675.593 674.292 -0.725677 -145.136 similary when i give g_energy -f npt.edr -o density.xvg the density option is not there to select it interactively. hence i am not able to plot the density graph.why? 1 Bond 2 Angle 3 Ryckaert-Bell. 4 LJ-14 5 Coulomb-14 6 LJ-(SR) 7 Disper.-corr. 8 Coulomb-(SR) 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 13 Conserved-En. 14 Temperature 15 Pressure-(bar) 16 Vir-XX 17 Vir-XY 18 Vir-XZ 19 Vir-YX 20 Vir-YY 21 Vir-YZ 22 Vir-ZX 23 Vir-ZY 24 Vir-ZZ 25 Pres-XX-(bar) 26 Pres-XY-(bar) 27 Pres-XZ-(bar) 28 Pres-YX-(bar) 29 Pres-YY-(bar) 30 Pres-YZ-(bar) 31 Pres-ZX-(bar) 32 Pres-ZY-(bar) 33 Pres-ZZ-(bar) 34 #Surf*SurfTen 35 Mu-X 36 Mu-Y 37 Mu-Z 38 T-System 39 Lamb-System and i have given my mdp file below. any help is highly appreciated. title = DCE NPT equilibration integrator = md nsteps = 200000 dt = 0.001 nstxout = 1000 nstvout = 1000 nstenergy = 1000 nstlog = 1000 constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ns_type = grid nstlist = 5 rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 coulombtype = PME pme_order = 4 fourierspacing = 0.16 tcoupl = V-rescale tc-grps = system tau_t = 0.1 ref_t = 300 pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 2.0 2.0 ref_p = 1.0 1.0 compressibility = 0.0 4.5e-5 pbc = xyz DispCorr = EnerPres gen_vel = no Regards Vinoth On Tue, Oct 26, 2010 at 5:33 AM, Dallas Warren <dallas.war...@monash.edu>wrote: > >I performed md simulation of 108 dichloroethane molecules in > isothermal-isobaric ensemble with the box size > > >3.002*2.17*2.17. after the simulation my box size has changed considerably > from the initial size to 2.87882 2.08095 > > >2.08095.why this happens? > > > > Density was obviously too lower under the conditions of the simulation. > Look at the change of pressure, volume and density for the box during that > simulation. > > > > >my second question is can i have a control over the box dimensions changes > during md (i.e when the box dimensions > > >changes during md i want to change it only on one axis(say x axis) and > want to keep the length of the other two axis (say > > >y and z) same as that of my initial box size? any help is highly > apprecited. > > > > Look at the pressure coupling settings, look at anisotropic pressure > coupling. > > > > Catch ya, > > Dr. Dallas Warren > > Medicinal Chemistry and Drug Action > > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3010 > dallas.war...@monash.edu > > +61 3 9903 9304 > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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