<div style="font-family: 'Times New Roman'; font-size: 16px;">Hi Nisha,<br _moz_dirty="" /><br _moz_dirty="" />I have performed a benchmark simulations of TIP3P water and I still obtained density 0.984g.cm-3. It looks that this model gives such a density. If you look at JCP 79, 926, 1983 you will see that the authors got 0.982g.cm-3 with MC. (Table 3) Try to evaluate alsoo other properties, each model of water has some deficiencies. I tried large number of cut-offs combinations LJ and QQ tyoes of interactions, but the density did not gange by more than 0.001g.cm-3. <br _moz_dirty="" /><br _moz_dirty="" />Greetings<br _moz_dirty="" /><br _moz_dirty="" />Zuzana<br /><br /><span>Dňa 03/31/10, nishap.patel@utoronto.ca napísal:</span><blockquote cite="mid:20100331135811.m9codqnpus8cwkks@webmail.utoronto.ca" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text plain">Hello,<br /><br /> So I looked at the manual and I changed my mdp parameters as follows to equilibrate at a constant pressure.<br /><br /> RUN CONTROL PARAMETERS =<br />integrator = sd<br />tinit = 0<br />dt = 0.002<br />nsteps = 500000<br />nstcomm = 1<br />nstxout = 0<br />nstvout = 0<br />nstfout = 0<br />nstlog = 500<br />nstenergy = 500<br />nstxtcout = 0<br />xtc-precision = 1000<br />nstlist = 5<br />ns_type = grid<br />pbc = xyz<br />rlist = 1.3<br />coulombtype = pme<br />rcoulomb = 1.3<br />epsilon-r = 1<br />vdw-type = switch<br />rvdw-switch = 1.0<br />rvdw = 1.2<br />DispCorr = EnerPres<br />fourierspacing = 0.1<br />fourier_nx = 0<br />fourier_ny = 0<br />fourier_nz = 0<br />pme_order = 6<br />ewald_rtol = 1e-06<br />epsilon_surface = 0<br />optimize_fft = no<br />tc_grps = system<br />tau_t = 0.1<br />ref_t = 298<br />Pcoupl = berendsen<br />tau_p = 1.0<br />compressibility = 4.5e-05<br />ref_p = 1.0<br />constraints = all-bonds<br />constraint-algorithm = Lincs<br />unconstrained-start = no<br />lincs-order = 4<br />lincs-warnangle = 30<br />lincs-iter = 1<br />gen_vel = yes<br />gen_temp = 298.0<br />gen_seed = 173529<br /><br />I also tried using mdp parameters as mentioned in some of the gromacs tutorials. I ran this simulation for 1ns and I am still getting density around 985g/l, which is low for tip3p water (27nm^3, 900 water molecules). I checked some of the publications and the values they obtained were ~998g/l. I checked for vacuum in my system, but I didn't see anything out of the ordinary. Any insights?<br /><br />Thanks<br /><br />Nisha P<br /><br /><br /><br />Quoting nishap.patel@utoronto.ca:<br /><br />>Thanks. I will look up the manual again.<br />><br />>Quoting Sander Pronk <pronk@cbr.su.se>:<br />><br />>>Hi Nisha,<br />>><br />>>Looking at your .mdp, there are some issues that might lead to the<br />>>behavior that you describe:<br />>>First: you should try to look up the published densities for tip3p<br />>>water at 300K - they might actually be close to what you get.<br />>>Second: your neighbor list cut-off (rlist) might be too small to<br />>>fully contain the charge groups (check the manual, section 7.3.11).<br />>>Third: You haven't enabled long-range mean field correction for the<br />>>pressure or energy. Expect the pressure to be strongly dependent on<br />>>cut-off (see the same section).<br />>><br />>>Sander<br />>><br />>><br />>>On Mar 30, 2010, at 22:47 , nishap.patel@utoronto.ca wrote:<br />>><br />>>>I have a box (3x3x3nm) of Tip3p water molecules ~900 and the<br />>>>density when I create the box using genbox is 997.177g/l. I did<br />>>>energy minimization run and the potential energy did converge<br />>>>smoothly, so I did NPT equilibration run of 100ps and I got the<br />>>>density value of 975g/l. Why does the density decrease after the<br />>>>run? these are the parameters that I used :<br />>>><br />>>>RUN CONTROL PARAMETERS<br />>>>integrator = md<br />>>>tinit = 0<br />>>>dt = 0.002<br />>>>nsteps = 50000<br />>>>nstcomm = 0<br />>>>nstxout = 0<br />>>>nstvout = 0<br />>>>nstfout = 0<br />>>>nstlog = 100<br />>>>nstenergy = 100<br />>>>nstxtcout = 0<br />>>>xtc_precision = 1000<br />>>>nstlist = 5<br />>>>ns-type = Grid<br />>>>pbc = xyz<br />>>>rlist = 1.1<br />>>>coulombtype = pme<br />>>>rcoulomb = 1.1<br />>>>epsilon-r = 1<br />>>>vdw-type = switch<br />>>>rvdw-switch = 0.8<br />>>>rvdw = 1.0<br />>>>Tcoupl = V-rescale<br />>>>tc-grps = System<br />>>>tau_t = 0.1<br />>>>ref_t = 300<br />>>>Pcoupl = berendsen<br />>>>tau_p = 0.5<br />>>>compressibility = 4e-05<br />>>>ref_p = 1.0<br />>>>constraints = all-bonds<br />>>>constraint-algorithm = Lincs<br />>>>unconstrained-start = no<br />>>>lincs-order = 4<br />>>>lincs-iter = 1<br />>>>lincs-warnangle = 30<br />>>><br />>>>Am I missing something?<br />>>>Thanks<br />>>><br />>>>Nisha Patel<br />>>><br />>>><br />>>>--<br />>>>gmx-users mailing list gmx-users@gromacs.org<br />>>><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br />>>>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br />>>>Please don't post (un)subscribe requests to the list. Use the<br />>>>www interface or send it to gmx-users-request@gromacs.org.<br />>>>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br />>><br />>>--<br />>>gmx-users mailing list gmx-users@gromacs.org<br />>><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br />>>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br />>>Please don't post (un)subscribe requests to the list. Use the<br />>>www interface or send it to gmx-users-request@gromacs.org.<br />>>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br />>><br />><br />><br />><br />>Nisha Patel<br />>MSc Candidate<br />>Leslie Dan Faculty of Pharmacy<br />>Department of Pharmaceutical Sciences<br />>144 College Street<br />>Room 1172<br />>Toronto, ON<br />>M5S 3M2<br />>Canada<br />>Telephone: 416-978-1536<br />><br />>--<br />>gmx-users mailing list gmx-users@gromacs.org<br />><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br />>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br />>Please don't post (un)subscribe requests to the list. Use the<br />>www interface or send it to gmx-users-request@gromacs.org.<br />>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br />><br /><br /><br /><br />Nisha Patel<br /><br /><br />-- <br />gmx-users mailing list gmx-users@gromacs.org<br /><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br />Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br />Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-request@gromacs.org.<br />Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br /></div></blockquote></div>