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Hi,<br><br>My last comment was not correct. Sorry, too many numbers in my head.<br>Both your density numbers are too low, more than can be explained by LJ cut-off settings.<br><br>How did you determine the density?<br>g_density does not give the correct number. The number in our paper for tip3p (not Charmm tip3p)<br>is incorrect, because Per used g_density, but g_density normalizes with the volume of the last frame<br>instead of the average volume over the simulation. I just fixed this for the next release.<br>I would always use g_energy to extract the density.<br><br>Berk<br><br><hr id="stopSpelling">From: gmx3@hotmail.com<br>To: gmx-users@gromacs.org<br>Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model<br>Date: Tue, 14 Sep 2010 11:58:31 +0200<br><br>
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Hi,<br><br>We did some checking.<br>The value of the density for tip3p reported in the Gromacs Charmm ff implementation of 1001.7 is incorrect.<br>This should have been 985.7. The number of 1014.7 for Charmm tip3p is correct.<br><br>I would expect that the difference with your number is mainly due to the shorter LJ cut-off you are using.<br><br>Berk<br><br><hr id="ecxstopSpelling">From: gmx3@hotmail.com<br>To: gmx-users@gromacs.org<br>Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model<br>Date: Tue, 14 Sep 2010 11:33:16 +0200<br><br>
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Hi,<br><br>I don't understand what exactly you want to reproduce.<br>Standard tip3p and Charmm tip3p are different models, so the density does not have to be identical.<br>The Gromacs Charmm FF implementation paper:<br>http://pubs.acs.org/doi/full/10.1021/ct900549r<br>gives 1002 for tip3p and 1015 for charmm tip3p (this is with LJ switched from 1 to 1.2 nm).<br>I have in an old paper 986 for tip3p, with 0.85 nm cut-off plus dispersion correction.<br>These numbers are quite different. I'll do some checking.<br><br>Berk<br><br>> Date: Tue, 14 Sep 2010 11:00:55 +0200<br>> From: spoel@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Regular vs. CHARMM TIP3P water model<br>> <br>> On 2010-09-14 10.23, Nicolas SAPAY wrote:<br>> > Hello everybody,<br>> ><br>> > I have many difficulties to reproduce TIP3P simulation results with CHARMM<br>> > TIP3P. Regular TIP3P gives systematically a lower density than its CHARMM<br>> > counterpart, independantly from the cutoff for non-bonded interactions,<br>> > the version of GROMACS (4.5.1 or 4.0.7) or the double precision.<br>> > Regular 961,067 +/-0,756 g/L<br>> > CHARMM 980,860 +/-0,492 g/L<br>> ><br>> > The Enthalpy of vaporization follows a similar scheme:<br>> > regular -39,992 +/-0,021 kJ/mol<br>> > CHARMM -40,665 +/-0,009 kJ/mol<br>> <br>> How about the dispersion correction?<br>> If that is not turned on densities will be too low (in both cases).<br>> <br>> ><br>> > In fact, CHARMM gives results closer to what I should obtain at 300K and 1<br>> > bar for TIP3P. I suspect an issue with the bond constraints, but I can't<br>> > locate precisely where it is. Settle parameters are exactly the same (as<br>> > well as constraints for flexible water). Did someone ever face a similar<br>> > problem?<br>> ><br>> > Rgards,<br>> > Nicolas<br>> ><br>> > P.S. I My system is just a box of 1728 water molecules pre-equilibrated<br>> > for 500 ps at 300 K and 1 bar.<br>> ><br>> > P.S. II I'm using the following simulation parameters:<br>> > constraints = hbonds<br>> > constraint_algorithm = LINCS<br>> > continuation = no<br>> > lincs-order = 4<br>> > lincs-iter = 1<br>> > lincs-warnangle = 30<br>> > morse = no<br>> > (LINCS or SHAKE should not make any difference since TIP3P is normally<br>> > treated by SETTLE).<br>> ><br>> > Other parameters are:<br>> > ; COUPLING<br>> > ; Temperature coupling<br>> > tcoupl = Berendsen<br>> > nsttcouple = -1<br>> > nh-chain-length = 10<br>> > tc_grps = System<br>> > tau_t = 0.1<br>> > ref_t = 300<br>> > ; Pressure coupling<br>> > pcoupl = Berendsen<br>> > pcoupltype = isotropic<br>> > nstpcouple = -1<br>> > tau_p = 1<br>> > compressibility = 4.5e-5<br>> > ref_p = 1<br>> ><br>> > ; NEIGHBORSEARCHING PARAMETERS<br>> > ; nblist update frequency<br>> > nstlist = 10<br>> > ns_type = grid<br>> > pbc = xyz<br>> > rlist = 1.15<br>> ><br>> > ; OPTIONS FOR ELECTROSTATICS AND VDW<br>> > ; Method for doing electrostatics<br>> > coulombtype = PME<br>> > rcoulomb-switch = 0<br>> > rcoulomb = 1.15<br>> > vdwtype = Cutoff<br>> > rvdw = 1.0<br>> > fourierspacing = 0.10<br>> > pme_order = 6<br>> > ewald_rtol = 1.0e-6<br>> > ewald_geometry = 3d<br>> > epsilon_surface = 0<br>> > optimize_fft = yes<br>> ><br>> > ; RUN CONTROL PARAMETERS<br>> > integrator = md<br>> > dt = 0.002<br>> > nsteps = 200000<br>> > comm_mode = Linear<br>> > nstcomm = 1<br>> > comm_grps = System<br>> ><br>> ><br>> <br>> <br>> -- <br>> David van der Spoel, Ph.D., Professor of Biology<br>> Dept. of Cell & Molec. Biol., Uppsala University.<br>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>> spoel@xray.bmc.uu.se http://folding.bmc.uu.se<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search 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 http://www.gromacs.org/Support/Mailing_Lists<br>
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