[gmx-users] TIP4p water in gromos force field files (OWT4 and IW)??
Justin A. Lemkul
jalemkul at vt.edu
Tue Feb 9 13:11:59 CET 2010
Rasmus Lundsgaard wrote:
> 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:
> #ifdef _FF_GROMACS
> 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
> #ifdef _FF_GROMOS96
> 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
> GROMACS release?
I think the possibility of implementation supersedes one's strict notions about
what should or should not be done (hence why they say Gromacs is "flexible").
You could do it if you want, but full implementation is not there, probably
because there has never been a widespread need for such a parameter set combination.
> Best regards
> Rasmus Lundsgaard
> 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
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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