<div style="font-family: 'Times New Roman'; font-size: 16px;">Hi Nisha,<br _moz_dirty="" /><br _moz_dirty="" />I did not try OPLSAA since I need TIP3P model with CHARMM. With this FF hydrogens are also considered as interaction sites. This is not very good combination for GROMACS, but it appeared that the differences are not too big and the time required for simulation with H interacttion side is significantly larger. <br _moz_dirty="" /><br _moz_dirty="" />From my experience rdf is not too sensitive to cut-offs. Try to estimate for instance dielectric constant, dipole moment, diffusion coefficient to be entirely sure. But I think you are getting equlibrated system. Good luck<br _moz_dirty="" /><br _moz_dirty="" />Zuzana <br /><br /><span>Dňa 04/01/10, nishap.patel@utoronto.ca napísal:</span><blockquote cite="mid:20100401104111.30b6a3j9r4kk8wg4@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">Hi Zuzana,<br /><br /> You are right. I did get my density to ~0.986g/cm3, and I actually came across this other paper by Price and Brooks, and initially they get a density of Tip3p using pme at around 0.979g/cm3, but they tweak some of the parameters in oplsaa to get the correct density. I am not sure if you have tried that and if that helps at all, but also they are using a different simulation package.<br /><br />I am getting good rdf values for the water even with slightly low density, so I guess it is okay.<br /><br />Thanks<br /><br />Quoting Zuzana Benkova <Zuzana.Benkova@savba.sk>:<br /><br />>Hi Nisha,<br />><br />>I have performed a benchmark simulations of TIP3P water and I still<br />>obtained density 0.984g.cm-3. It looks that this model gives such a<br />>density. If you look at JCP 79, 926, 1983 you will see that the<br />>authors got 0.982g.cm-3 with MC. (Table 3) Try to evaluate alsoo<br />>other properties, each model of water has some deficiencies. I tried<br />>large number of cut-offs combinations LJ and QQ tyoes of<br />>interactions, but the density did not gange by more than 0.001g.cm-3.<br />><br />><br />>Greetings<br />><br />>Zuzana<br />><br />>Dňa 03/31/10, nishap.patel@utoronto.ca napísal:Hello,<br />><br />> So I looked at the manual and I changed my mdp parameters as<br />>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<br />>tutorials. I ran this simulation for 1ns and I am still getting<br />>density around 985g/l, which is low for tip3p water (27nm^3, 900<br />>water molecules). I checked some of the publications and the values<br />>they obtained were ~998g/l. I checked for vacuum in my system, but I<br />>didn't see anything out of the ordinary. Any insights?<br />><br />>Thanks<br />><br />>Nisha P<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>[1]<br />>>>>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a>[2]<br />>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>[3]<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>[4]<br />>>>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a>[5]<br />>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>[6]<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>[7]<br />>>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a>[8] before<br />>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>[9]<br />>><br />><br />>Nisha Patel<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>[10]<br />>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a>[11] before<br />>posting!<br />>Please don't post (un)subscribe requests to the list. Use thewww<br />>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>[12]<br />><br />><br />>Links:<br />>------<br />>[1] <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br />>[2] <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a><br />>[3] <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br />>[4] <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br />>[5] <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a><br />>[6] <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br />>[7] <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br />>[8] <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a><br />>[9] <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br />>[10] <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br />>[11] <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a><br />>[12] <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 />-- <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>