[gmx-users] Regular vs. CHARMM TIP3P water model
gmx3 at hotmail.com
Tue Sep 14 11:33:16 CEST 2010
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:
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.
> 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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