[gmx-users] Regular vs. CHARMM TIP3P water model
Berk Hess
gmx3 at hotmail.com
Tue Sep 14 13:25:47 CEST 2010
Hi,
The choice of constraint algorithm is irrelevant for the results.
As I understood Charmm tip3p has less structure than standard tip3p
and it would not surprise me if the density is different.
But I have never closely looked at Charmm tip3p properties myself.
Berk
> Date: Tue, 14 Sep 2010 13:11:47 +0200
> Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model
> From: nicolas.sapay at cermav.cnrs.fr
> To: gmx-users at gromacs.org
>
> >
> > 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
>
> Actually, TIP3P and CHARMM TIP3P are supposed to give (almost) identical
> results as they are not exactly different models but different
> implementations of a same model. That is why I'm surprised of the rather
> large difference in the density values observed in my simulations or in
> the JCTC paper.
>
> In CHARMM, the additionnal Lennard-Jones parameters for the TIP3P hydrogen
> are not here to better reproduce water properties but for practical
> purpose - normally, the hydrogens are almost entirely included in the
> oxygen VDW radius. As far as I understand, those parameters are here to
> improve the stability of simulations by limiting artificial close contacts
> between a large negative charge and the point charge on the hydrogen
> atoms.
>
> In fact, I was wondering if the Settle algorithm is appropriate to CHARMM
> TIP3P. In the original CHARMM RTF file, there is a SHAKE constraint on the
> H-H distance which is not present in the GROMACS tips3p.itp file. So, a
> better use of the CHARMM TIP3P model in GROMACS would be to add this
> constraint in tips3p.itp and use Shake instead of Settle, isn't it?
>
> >
> >> Date: Tue, 14 Sep 2010 11:00:55 +0200
> >> From: spoel at xray.bmc.uu.se
> >> To: gmx-users at 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.
> >> spoel at xray.bmc.uu.se http://folding.bmc.uu.se
> >> --
> >> gmx-users mailing list gmx-users at 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-request at gromacs.org.
> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > --
> > gmx-users mailing list gmx-users at 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-request at 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 at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100914/d5ecff12/attachment.html>
More information about the gromacs.org_gmx-users
mailing list