[gmx-users] custom forcefields or a new forcefields

[DreamCatcher]

Message: 5
Date: Thu, 01 Apr 2010 16:30:44 +1100
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] custom forcefields or a new forcefields
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4BB42F84.9050703 at anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 01/04/10 16:20, DreamCatcher wrote:
> Hello gmx-users,
>         I have just look through the mail-list to find this
> http://lists.gromacs.org/pipermail/gmx-users/2009-October/045569.htmlconcerned
> on the develop of a new force field.
>         It seems that If I wanna use a force field haven't been
> incooperate into the gromacs' extant version, What I need to do only is
> to make some new files with suffixes like .rtp / .hdb / nb.itp / bon.itp
> to contain the new force field parameters.
Yes.
> This may certainly work out
> for pdb2gmx programme, But will it also work out for another programmes
> like mdrun?
Well, it will, because pdb2gmx builds topologies that grompp can parse
into input for mdrun.
> Cause maybe the forcefield potential function are different
> from any other forcefileds contained in the gromacs. Then what others
> can I do to finally introduce a totally new force field to gromacs?
Have a look at all the possibilities GROMACS already knows about in
chapter 4, and consider also the use of table-lookups for two-body
functions (manual 6.7.2). IIRC many-bodied functions won't work yet.

Mark
------------------------------

Hey Mark,
       Thanks very much for your benevolence. Another question, How can I
set up a new functions? Where should they be located? What do you mean when
you talk about "table-lookups  for two-body functions"? Where should the
lookups take place?
       When I use "man mdrun" to find a "-table" option for table-lookup, it
obviously indicates an input file **.xvg, What can **.xvg file do? How
should it be created? What is the content in it?
       Thank a lot and thanks in advance!

celeste

2010-4-1
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