[gmx-users] custom forcefields or a new forcefields

Mark Abraham Mark.Abraham at anu.edu.au
Thu Apr 1 15:19:59 CEST 2010

On 1/04/2010 9:08 PM, DreamCatcher wrote:
> Message: 5
> Date: Thu, 01 Apr 2010 16:30:44 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto: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
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <4BB42F84.9050703 at anu.edu.au
> <mailto: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.html
> concerned
>  > 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!

Read the manual sections I listed. I didn't do that for my own 


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