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