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

[Amit Choubey]

By the way thank you very much for answering my questions.

Amit

On Tue, Sep 8, 2009 at 7:13 PM, Amit Choubey <kgp.amit at gmail.com> 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.
>
> 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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>
>
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