[gmx-users] Vacuum FF in Gromacs-4.0.5

David van der Spoel spoel at xray.bmc.uu.se
Fri Jan 29 08:34:49 CET 2010

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) 
Phys. Chem. Chem. Phys. 11 pp. 8069-8078 (2009) 

> Berk
> ------------------------------------------------------------------------
> Date: Fri, 29 Jan 2010 12:23:02 +0530
> From: pdnikhil at yahoo.co.in
> To: gmx-users at 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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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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