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

[David van der Spoel]

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