On 1/29/10 8:29 AM, Berk Hess wrote:
Hi,
I removed this force field on purpose.
The name is already very confusing. It is not a vacuum force field at all.
It is an implicit solvent force field, but a quite bad one.
It only scales down the charges on groups with net charge.
If you really want to simulate a protein in vacuum do NOT use this force
field.
If you really, really want to use this force field, download an old Gromacs
distribution and copy the parameter files.
It depends on what you want to do. If you want to simulate what happens
to a protein under vacuum conditions you could use a normal force field,
but you have to consider which sidechains are charged. See e.g.:
Biochemistry 46 pp. 933-945 (2007)
http://pubs.acs.org/cgi-bin/download.pl?bi061182y/B6CC
or
Phys. Chem. Chem. Phys. 11 pp. 8069-8078 (2009)
http://dx.doi.org/10.1039/b903846a
Berk
------------------------------------------------------------------------
Date: Fri, 29 Jan 2010 12:23:02 +0530
From: pdnik...@yahoo.co.in
To: gmx-users@gromacs.org
Subject: [gmx-users] Vacuum FF in Gromacs-4.0.5
Hi,
I wanted to inquire about the vacuum FF distributed officially with
GROMACS-4.0.5. I wish to carry out a vacuum MD of ~300 aa protein
FF.dat file mentions of G43b1 as officially distributed vacuum FF. But
there are no FF related files-.rtp,.hdb etc present. Is that the case
that GROMACS-4 is improperly installed at my end or do I have to get
these FF files from some external source ?
Regards,
Nikhil
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