[gmx-users] Regular vs. CHARMM TIP3P water model
Nicolas SAPAY
nicolas.sapay at cermav.cnrs.fr
Tue Sep 14 15:49:03 CEST 2010
>
> 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: gmx3 at hotmail.com
> To: gmx-users at 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: 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
> --
> 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
More information about the gromacs.org_gmx-users
mailing list