Force field for fully flexible water

[Axel]

On Oct 7, 12:58 pm, nadler <rod... at gmx.ch> wrote:
> Hi all
>
> Recently I have seen a force field that allows the calculation of
> fully flexible water molecules, which I'd like to use (X.B. Zhang in
> Fluid Phase Equilibria 262 (2007) p. 210). The problem is that when
> running a test, the molecules just "explode" and I did not find out
> why. The input is as follows. The uncommented lines are resulting from
> an attempt to apply restraints, which did not work as well. The
> molecules again "exploded". Can anyone help me with that? Thanks!


try a shorter time step. 1.0fs is far too large for
a fully flexible water potential, especially, if your
initial configuration is not in equilibrium. i'd begin
with 0.25fs or less. and perhaps also use a CSVR thermostat
with a short time constant instead of a NOSE.

cheers,
    axel.

>
> Cheers, Roger.
>
> &FORCE_EVAL
>   METHOD FIST
>   &MM
>     &FORCEFIELD
> #      &BEND
> #        ATOMS H O H
> #        K 0.
> #        THETA0 1.8
> #      &END BEND
> #      &BOND
> #        ATOMS O H
> #        K 0.
> #        R0 1.8
> #      &END BOND
>       &BEND
>         ATOMS H O H
>         KIND HARMONIC
>         K [kjmol*deg^-2] 353.0
>         THETA0 [deg] 109.4712
>       &END BEND
>       &BOND
>         ATOMS O H
>         KIND HARMONIC
>         K [kjmol*angstrom^-2] 1480.0
>         R0 [angstrom] 0.9611
>       &END BOND
>       &CHARGE
>         ATOM O
>         CHARGE -0.8476
>       &END CHARGE
>       &CHARGE
>         ATOM H
>         CHARGE 0.4238
>       &END CHARGE
>       &NONBONDED
>         &LENNARD-JONES
>           atoms O O
>           EPSILON [kjmol] 0.6287
>           SIGMA 3.1169
>           RCUT 10.0
>         &END LENNARD-JONES
>         &LENNARD-JONES
>           atoms O H
>           EPSILON [kjmol] 0.142723
>           SIGMA 2.04845
>           RCUT 10.0
>         &END LENNARD-JONES
>         &LENNARD-JONES
>           atoms H H
>           EPSILON [kjmol] 0.0324
>           SIGMA 0.98
>           RCUT 10.0
>         &END LENNARD-JONES
>       &END NONBONDED
>     &END FORCEFIELD
>     &POISSON
>       &EWALD
>         EWALD_TYPE spme
>         ALPHA .35
>         GMAX 25
>         O_SPLINE 4
>       &END EWALD
>     &END POISSON
>   &END MM
>   &SUBSYS
>     &CELL
>       ABC 24.955 24.955 24.955
>       UNIT ANGSTROM
>     &END CELL
>     &COORD
>    O  22.9836691917178939 6.93183557997552668 0.754607553842305823
> H2O
>    H  23.1493887587765457 6.38145839360815526 1.57291188465716791
> H2O
>    H  23.8522379765498265 7.11351376960166615 0.293542155628028989
> H2O
>    O  9.55748115579216773 10.1625527712466361 -12.8321807856825103
> H2O
>    H  9.48825863164111638 10.8031673228011336 -13.5969168437373611
> H2O
>    H  8.66207900403075648 9.75244702889359871 -12.6587787478834102
> H2O
>    O  19.8436465738885985 10.0378451904347870 9.93036518412813862
> H2O
>    H  19.1357369126550836 9.37699136789161081 9.68109397285001450
> H2O
>    H  19.9908902622388958 10.0115791753817565 10.9191166153261410
> H2O
>     &END COORD
> #    &COLVAR
> #      &DISTANCE
> #        ATOMS 1 2
> #      &END DISTANCE
> #    &END COLVAR
> #    &COLVAR
> #      &DISTANCE
> #        ATOMS 1 3
> #      &END DISTANCE
> #    &END COLVAR
> #    &COLVAR
> #      &ANGLE
> #        ATOMS 2 1 3
> #      &END ANGLE
> #    &END COLVAR
>   &END SUBSYS
> &END FORCE_EVAL
> &GLOBAL
>
>   PROJECT water
>   RUN_TYPE md
> &END GLOBAL
> &MOTION
> #  &CONSTRAINT
> #    &COLLECTIVE
> #      TARGET [angstrom]  0.9611
> #      MOLNAME H2O
> #      COLVAR 1
> #      &RESTRAINT
> #        K [kjmol*angstrom^-2] 1480.0
> #      &END RESTRAINT
> #    &END COLLECTIVE
> #    &COLLECTIVE
> #      TARGET [angstrom]  0.9611
> #      MOLNAME H2O
> #      COLVAR 2
> #      &RESTRAINT
> #        K [kjmol*angstrom^-2] 1480.0
> #      &END RESTRAINT
> #    &END COLLECTIVE
> #    &COLLECTIVE
> #      TARGET [deg]  109.4712
> #      MOLNAME H2O
> #      COLVAR 3
> #      &RESTRAINT
> #          K   [kjmol*deg^-2]  353.0
> #      &END
> #    &END COLLECTIVE
>   &END CONSTRAINT
>   &MD
>     ENSEMBLE NVT
>     STEPS 100
>     TIMESTEP 1.0
>     TEMPERATURE 298
>     &THERMOSTAT
>       REGION MOLECULE
>       &NOSE
>         LENGTH 3
>         YOSHIDA 3
>         TIMECON 1000
>         MTS 2
>       &END NOSE
>     &END
>   &END MD
> &END MOTION