> > 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.
That's a good thing to know, I'll recalculate the density with g_energy. > > 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? 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? Read http://www.gromacs.org/Support/Mailing_Lists
