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Hi,<br><br>The choice of constraint algorithm is irrelevant for the results.<br><br>As I understood Charmm tip3p has less structure than standard tip3p<br>and it would not surprise me if the density is different.<br>But I have never closely looked at Charmm tip3p properties myself.<br><br>Berk<br><br>> Date: Tue, 14 Sep 2010 13:11:47 +0200<br>> Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model<br>> From: nicolas.sapay@cermav.cnrs.fr<br>> To: gmx-users@gromacs.org<br>> <br>> ><br>> > 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<br>> > 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<br>> > from 1 to 1.2 nm).<br>> > I have in an old paper 986 for tip3p, with 0.85 nm cut-off plus dispersion<br>> > correction.<br>> > These numbers are quite different. I'll do some checking.<br>> ><br>> > Berk<br>> <br>> Actually, TIP3P and CHARMM TIP3P are supposed to give (almost) identical<br>> results as they are not exactly different models but different<br>> implementations of a same model. That is why I'm surprised of the rather<br>> large difference in the density values observed in my simulations or in<br>> the JCTC paper.<br>> <br>> In CHARMM, the additionnal Lennard-Jones parameters for the TIP3P hydrogen<br>> are not here to better reproduce water properties but for practical<br>> purpose - normally, the hydrogens are almost entirely included in the<br>> oxygen VDW radius. As far as I understand, those parameters are here to<br>> improve the stability of simulations by limiting artificial close contacts<br>> between a large negative charge and the point charge on the hydrogen<br>> atoms.<br>> <br>> In fact, I was wondering if the Settle algorithm is appropriate to CHARMM<br>> TIP3P. In the original CHARMM RTF file, there is a SHAKE constraint on the<br>> H-H distance which is not present in the GROMACS tips3p.itp file. So, a<br>> better use of the CHARMM TIP3P model in GROMACS would be to add this<br>> constraint in tips3p.itp and use Shake instead of Settle, isn't it?<br>> <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<br>> >> CHARMM<br>> >> > TIP3P. Regular TIP3P gives systematically a lower density than its<br>> >> CHARMM<br>> >> > counterpart, independantly from the cutoff for non-bonded<br>> >> 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<br>> >> and 1<br>> >> > bar for TIP3P. I suspect an issue with the bond constraints, but I<br>> >> can't<br>> >> > locate precisely where it is. Settle parameters are exactly the same<br>> >> (as<br>> >> > well as constraints for flexible water). Did someone ever face a<br>> >> similar<br>> >> > problem?<br>> >> ><br>> >> > Rgards,<br>> >> > Nicolas<br>> >> ><br>> >> > P.S. I My system is just a box of 1728 water molecules<br>> >> 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<br>> >> 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>> > --<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at<br>> > 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>> <br>> <br>> -- <br>> [ Nicolas Sapay - Post-Doctoral Fellow ]<br>> CERMAV - www.cermav.cnrs.fr<br>> BP53, 38041 Grenoble cedex 9, France<br>> Phone: +33 (0)4 76 03 76 44/53<br>> <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> </body>
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