[gmx-users] buckingham potentials

[sreelakshmi ramesh]

Dear justin,
                   I have no clues  about rewriting a force field so i think
i can t proceed with this anymore.

thanks a lot for your patient reply.
sree.



On Wed, Dec 22, 2010 at 9:32 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> sreelakshmi ramesh wrote:
>
>> Dear justin,
>>                 I am sorry the file is ffG43a1nb.itp.It <
>> http://ffG43a1nb.itp.It> was a typing mistake.
>>
>>
> The points I raised before still stand:
>
> 1. You're not using 43A1, you're using ffgmx, according to that message
> from grompp.
>
> 2. You can't make a simple change to any of the force fields included in
> Gromacs to magically convert them into using Buckingham potentials.  None of
> them were designed to do that.  You'll have to basically re-write the
> entirety of the ff*nb.itp file, and then validate that such a force field
> model is even valid, because none of them were parameterized to be.
>
> -Justin
>
>  On Wed, Dec 22, 2010 at 9:26 AM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    Justin A. Lemkul wrote:
>>
>>
>>
>>        sreelakshmi ramesh wrote:
>>
>>            I am using gromos force field fotr my work and This force
>>            field's files come filled
>>             with LJ  functions and now if i want to work with
>>            buckingham potential i changed in default section of force
>>            field ffG34a21.itp file but it gives me the follwing errors
>>
>>
>>            ERROR 77 [file ffgmxnb.itp, line 144]:
>>             Trying to add LJ (SR) while the default nonbond type is
>>            Buck.ham (SR)
>>
>>
>>    I should also add that if you think you're using Gromos96 (although
>>    from "ffG34a21.itp" it's not at all clear to me that you're using
>>    any legitimate form of it - 43A1? 43A2? something else?), you're
>>    not.  The "ffgmx" force field is a modified form of Gromos87 that is
>>    antiquated and should not be used for new simulations, as described
>>    in detail in the manual.
>>
>>    -Justin
>>
>>
>>    --     ========================================
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    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
> MILES-IGERT Trainee
> 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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