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
#endif
#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
#endif
...
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?
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.
-Justin
Best regard!
Rasmus
--
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: [email protected]
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