[gmx-users] TIP4p water in gromos force field files (OWT4 and IW)??
RAL at kt.dtu.dk
Tue Feb 9 13:08:49 CET 2010
Dear Justin (and the rest)
I have been using the TIP4p water model with OPLS-AA and TraPPE - and
now for comparison I would like to try with the Gromos force field. From
the TIP4p.itp file in the /shared/top directory it states:
1 OWT4 1 SOL OW 1 0.0
2 HW 1 SOL HW1 1 0.52
3 HW 1 SOL HW2 1 0.52
4 IW 1 SOL MW 1 -1.04
1 OWT4 1 SOL OW 1 0.0 15.9994
2 H 1 SOL HW1 1 0.52 1.008
3 H 1 SOL HW2 1 0.52 1.008
4 IW 1 SOL MW 1 -1.04 0.0
So from this it should be implemented in the GROMACS gromos nb and bon
files - right?!? I mean that the OTW4 and IW are in the ffgmxnb,
ffgmxbon (hence the ifdef _FF_GROMACS).
What I mean is that if it's very rare to use gromos with TIP4p water
models (and maybe even not a strictly correct use of the force field),
why is it then mentioned in the TIP4p.itp example file in the official
Justin A. Lemkul wrote:
> Rasmus Lundsgaard wrote:
>> Dear all
>> I would like to do some simulation with the TIP4p water model with
>> the ffG53a6 (Gromos96) force field.
>> In *TIP4p.itp* it states to use the *OWT4* atom for the oxygen and
>> the *IW* for the charged atom (4 site water model), but these two
>> atoms are not listed in the *ffG53a6nb.itp* and *ffG53a6bon.itp*
>> files. This means that GROMACS can not find these atoms and how to
>> calculate LJ and bonded forces with these atoms...
>> Have I overseen something or are they suddenly lost from the gromos
>> itp's in GROMACS??
>> The OW atom in the itp's are for the SPC/E water model - so they are
>> not use able for TIP4p (different LJ parameters)
> I don't know that I've seen anyone do a simulation with
> Gromos96+TIP4P. The original derivation of Gromos96 (and the most
> common usage) is Gromos96+SPC or SPC/E. If you're set on using TIP4P
> as your water model, you'd better be ready to provide justification
> for that choice.
> If you need to add atom types, you certainly can, but you may have to
> re-name them so as not to conflict with existing SPC or SPC/E atom
> types. It's very simple to put these parameters in the nb.itp,
> bon.itp, and .atp files.
>> Best regard!
>> PhD student at "Center for Energy Resources Engineering" (CERE-DTU)
>> Department of Chemical and Biochemical Engineering, Building 229
>> Technical University of Denmark - DTU
>> DK - 2800 Lyngby, Denmark
>> Email: RAL at kt.dtu.dk
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