[gmx-users] how to use a new force field

[Tsjerk Wassenaar]

Hi,

Well, to *add* a new force field, summerizing and extending the
replies given earlier, you edit the file FF.dat in the directory
$GMXPATH/share/gromacs/top.This file looks like

11
ffG43a1  GROMOS96 43a1 force field
ffG43b1  GROMOS96 43b1 vacuum force field
ffG43a2  GROMOS96 43a2 force field (improved alkane dihedrals)
ffG45a3  GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
ffG53a5  GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
ffG53a6  GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
ffoplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
ffgmx    [DEPRECATED] Gromacs force field (see manual)
ffgmx2   [DEPRECATED] Gromacs force field with hydrogens for NMR
ffencadv Encad all-atom force field, using scaled-down vacuum charges
ffencads Encad all-atom force field, using full solvent charges

Raise the number with one and add a line, for instance:

ffAmit AMIT Amits new and improved force field

Then create the files that contain your force field. Definitely the
ones that describe the atom types, the overall parameters and bonded
and non-bonded parameters.

ffAmit.atp
ffAmit.itp
ffAmitbon.itp
ffAmitnb.itp

Possibly also the files related to building blocks, hydrogen bond
addition and dealing with termini:

ffAmit.rtp
ffAmit.hdb
ffAmit-c.tdb
ffAmit-n.tdb

And maybe also a file for generation of virtual sites.

ffAmit.ddb

To know what to put in which file, look at the existing ones and dig
through chapter 5 of the manual. Note also that you can put all these
files with a consistent name in the $GMXLIB directory, so that pdb2gmx
knows where to search.

Hope it helps.

Cheers,

Tsjerk

On Wed, Sep 9, 2009 at 5:09 AM, Amit Choubey<kgp.amit at gmail.com> wrote:
> Thank you v. much for the replies. I will try to set that up.
>
> Amit
>
> On Tue, Sep 8, 2009 at 6:57 PM, Dallas B. Warren
> <Dallas.Warren at pharm.monash.edu.au> wrote:
>>
>> Best if you don't mess with the ones that are installed.  Set up your own
>> forcefield files in a local directory and edit those, GROMACS scripts will
>> then look in the local directory first, before going to the installed one.
>>
>> Catch ya,
>>
>> Dr. Dallas Warren
>> Department of Pharmaceutical Biology
>> Pharmacy and Pharmaceutical Sciences, Monash University
>> 381 Royal Parade, Parkville VIC 3010
>> dallas.warren at pharm.monash.edu.au
>> +61 3 9903 9167
>> ---------------------------------
>> When the only tool you own is a hammer, every problem begins to resemble a
>> nail.
>>
>> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
>> On Behalf Of Amit Choubey
>> Sent: Wednesday, 9 September 2009 11:53 AM
>> To: jalemkul at vt.edu; Discussion list for GROMACS users
>> Subject: Re: [gmx-users] how to use a new force field
>>
>> Hi,
>>
>> so is it a good idea to edit the original gromacs files in top directory
>> for introducing new force field or is there a way to compliment the existing
>> FF files by a new file made by me?
>>
>> Amit
>>
>> On Tue, Sep 8, 2009 at 2:38 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> Amit Choubey wrote:
>> hi gromacs user,
>>
>> Is there any good way to introduce new force field in the gromacs library?
>>
>> Read in the manual about the organization of existing force fields, as
>> well as the component files that are necessary to make it function.  Beyond
>> that, look at the implemented force fields themselves and see how they work
>> together.
>>
>> -Justin
>> Amit
>>
>> ------------------------------------------------------------------------
>>
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>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623