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