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

[Amit Choubey]

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.

Amit

On Tue, Sep 8, 2009 at 6:58 PM, Justin A. Lemkul <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>> 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> | (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
>
> ========================================
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