[gmx-users] Regular vs. CHARMM TIP3P water model

Nicolas SAPAY nicolas.sapay at cermav.cnrs.fr
Tue Sep 14 13:13:55 CEST 2010 

>
> 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: 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 11:58:31 +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: 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
>> --
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-- 
[ Nicolas Sapay - Post-Doctoral Fellow ]
CERMAV - www.cermav.cnrs.fr
BP53, 38041 Grenoble cedex 9, France
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