[gmx-users] custom forcefields or a new forcefields
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
> > 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.
> > 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.
> 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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