[gmx-users] Re: Force field parameters in water or in vacuum?

[Chih-Ying Lin]

Hi
for  45a3 force field, is it created in vacuum / in water or solution ?
Justin said the most of the force field is defined as condensed phase ???
Do you mean the liquid phase / or in water phase ?

Thanks

Lin





Message: 7
Date: Thu, 22 May 2008 13:13:37 -0400
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] Force field parameters in water or in vacuum?
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <1211476417.4835a9c19e92b at webmail.vt.edu>
Content-Type: text/plain; charset=ISO-8859-1

Quoting Chih-Ying Lin <chihying2008 at gmail.com>:

> Hi
> For one molecule, will Gromacs give the same set of force field
> parameters to this molecule no matter this molecule is put in water or
> in vacuum?

Depending on what's defined within the specific force field, yes.  For example,
ffG43b1 is a "vacuum forcefield," whereas most others are parameterized for use
with condensed phases.

> The bond length, the bond angle, and the dihedral angles of the same
> molecule will be different in water and in vacuum.
> So, will the force field parameters be changed/ adjusted in water than
> in vacuum?

There's no decision structure that Gromacs will magically use to determine
what's in your system.  All the parameters are pre-defined in the relevant .rtp
and .itp files in $GMXLIB/top.

>
>
> How does Gromacs set the force field parameters for the molecule?
> I mean..... are the force field paramters determined in local or in global?
> Could I change parts of  the force field parameters which I found from
> the published paper?

The location of your files will depend on how Gromacs was installed, but can
always be found in $GMXLIB/top.  If you want to make changes to an existing set
of parameters, it is best to copy the relevant .rtp, .itp, etc. files into your
working directory and alter then there.

> Or, I could not change parts of the force field parameters; instead, I
> have to change the whole set of the force field
> parameters???

Well, I wouldn't make random changes to things :-)  The changes you make have to
be compatible with the functional form and derivation of the force field.
Otherwise, anything you do would probably be somewhat questionable.

-Justin

>
>
> Thank you
> Lin
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========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================



On 5/22/08, Chih-Ying Lin <chihying2008 at gmail.com> wrote:
> Hi
>  For one molecule, will Gromacs give the same set of force field
>  parameters to this molecule no matter this molecule is put in water or
>  in vacuum?
>  The bond length, the bond angle, and the dihedral angles of the same
>  molecule will be different in water and in vacuum.
>  So, will the force field parameters be changed/ adjusted in water than
>  in vacuum?
>
>
>  How does Gromacs set the force field parameters for the molecule?
>  I mean..... are the force field paramters determined in local or in global?
>  Could I change parts of  the force field parameters which I found from
>  the published paper?
>  Or, I could not change parts of the force field parameters; instead, I
>  have to change the whole set of the force field
>  parameters???
>
>
>  Thank you
>
> Lin
>