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

[Justin A. Lemkul]

Amit Choubey wrote:
> hi,
> 
> ok the next question that bugs me is if i make a directory consisting of 
> my modified force field (*.atp, *.rtp, *bon.itp,*nb.itp) and i want to 
> use pdb2gmx to get the *.top & .gro files according to the above new FF 
> files, how do i supply this info to pdb2gmx. In other words how do i 
> make pdb2gmx aware of the new FF files.
> 

Make a new entry in (a local copy of) FF.dat.

-Justin

> Amit
> 
> On Tue, Sep 8, 2009 at 6:58 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Amit Choubey wrote:
> 
>         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?  
> 
> 
>     It is generally better to not mess with system-level force field
>     files unless you're very sure of what you're doing, and experienced
>     in making such changes. If you alter one of the original force field
>     files, and you don't do it right, reverting the changes is often
>     difficult.  If, for example, you want to modify the OPLS-AA force
>     field, do not ever make any changes to the original file, instead
>     implement them in files like ffoplsaa_mod.*
> 
>     It is even safer to implement your changes in the local directory
>     until you are confident everything is working properly, then if
>     you're comfortable that you've done everything 100% right, move your
>     files into /share/top for convenience later.
> 
>     -Justin
> 
> 
>         Amit
> 
> 
>         On Tue, Sep 8, 2009 at 2:38 PM, Justin A. Lemkul
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto: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 <http://vt.edu> <http://vt.edu> | (540)
>         231-9080
> 
>            http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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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

========================================