Hi Nisha, Looking at your .mdp, there are some issues that might lead to the behavior that you describe: First: you should try to look up the published densities for tip3p water at 300K - they might actually be close to what you get. Second: your neighbor list cut-off (rlist) might be too small to fully contain the charge groups (check the manual, section 7.3.11). Third: You haven't enabled long-range mean field correction for the pressure or energy. Expect the pressure to be strongly dependent on cut-off (see the same section).
Sander On Mar 30, 2010, at 22:47 , nishap.pa...@utoronto.ca wrote: > I have a box (3x3x3nm) of Tip3p water molecules ~900 and the density when I > create the box using genbox is 997.177g/l. I did energy minimization run and > the potential energy did converge smoothly, so I did NPT equilibration run of > 100ps and I got the density value of 975g/l. Why does the density decrease > after the run? these are the parameters that I used : > > RUN CONTROL PARAMETERS > integrator = md > tinit = 0 > dt = 0.002 > nsteps = 50000 > nstcomm = 0 > nstxout = 0 > nstvout = 0 > nstfout = 0 > nstlog = 100 > nstenergy = 100 > nstxtcout = 0 > xtc_precision = 1000 > nstlist = 5 > ns-type = Grid > pbc = xyz > rlist = 1.1 > coulombtype = pme > rcoulomb = 1.1 > epsilon-r = 1 > vdw-type = switch > rvdw-switch = 0.8 > rvdw = 1.0 > Tcoupl = V-rescale > tc-grps = System > tau_t = 0.1 > ref_t = 300 > Pcoupl = berendsen > tau_p = 0.5 > compressibility = 4e-05 > ref_p = 1.0 > constraints = all-bonds > constraint-algorithm = Lincs > unconstrained-start = no > lincs-order = 4 > lincs-iter = 1 > lincs-warnangle = 30 > > Am I missing something? > Thanks > > Nisha Patel > > > -- > 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/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/mailing_lists/users.php -- 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/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/mailing_lists/users.php
