Good. I just calculated tip3p energies for a Charmm tip3p trajectory. Standard tip3p gives 1.1 kJ/mol per water molecule higher energies. Thus the LJ on H's gives significant extra attraction which increases the density.
Berk > Date: Tue, 14 Sep 2010 15:49:03 +0200 > Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model > From: nicolas.sa...@cermav.cnrs.fr > To: gmx-users@gromacs.org > > > > > > 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 have just done a quick test using dispersion correction > (DispCorr=EnerPres) and the density value extracted from the edr file by > g_energy. I obtain fairly similar results: 984.8 +/-4.5 for TIP3P and > 1015.0 +/- 3.6 for Charmm TIP3P. > > > > > 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? 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? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > [ Nicolas Sapay - Post-Doctoral Fellow ] > CERMAV - www.cermav.cnrs.fr > BP53, 38041 Grenoble cedex 9, France > Phone: +33 (0)4 76 03 76 44/53 > > -- > 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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