> > 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.
Great, I obtain a similar result: -40.0 kJ/mol for regular tip3p vs -41.2 kJ/mol for Charmm tip3p (so a difference of 1.2 kJ/mol in favor of Charmm tip3p). By the way, I have noted that the SHAKE force constants are different between Gromacs and Charmm. In the Gromacs implementation, the constant is 376560 kJ/mol/A^2 for the O-H bond and 460,24 kJ/mol/rad^2 for the H-O-H angle. In the Charmm parameter file, the force constant is 188280 kJ/mol/A^2 for the bond (2 times lower) and 23012 kJ/mol/rad^2 for the angle (50 times higher). Is there a justification for that? > > 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? 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
