[gmx-users] calculate potential with tabulated non-bonded interactions

[Liu, Liang]

Well my first question is: if the pdb2gmx command must take a force file? I
guess it should be necessary. Then the available list contains amber and
others, but not user-specified potential. This will affect the future
simulation or calculation?

On Thu, Nov 17, 2011 at 10:06 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Liu, Liang wrote:
>
>> Well, I already have the xvg files from others. However I don't know how
>> to use it.
>>
>>
> Start with the manual, where modifications to the topology and relevant
> commands and files are described.  Then refer to the how-to online, which
> has specific instructions.  Then, ask specific questions of problems you
> are having.  I doubt anyone on this list will be able or willing to guess
> where your problems are at this point.
>
> -Justin
>
>  On Thu, Nov 17, 2011 at 10:00 AM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    Liu, Liang wrote:
>>
>>        Dear all,
>>
>>        I am trying to calculate potentials for RNA structures with a
>>        serial of tabulated potentials (non-bonded).
>>        And the only potential I am going to use is the tabulated
>>        potentials, and the effect from force field should be removed.
>>        However, when I use pdb2gmx to build the topology file, I have
>>        to choose a force field. What should I do for that? Thanks.
>>
>>
>>    It sounds like you need to be constructing your own force field,
>>    completely, from scratch.  If you're not looking to use the existing
>>    force fields, this sounds like the only real solution.  You can take
>>    the time to make .xvg files for bonded and nonbonded interactions
>>    (see the manual), but that is probably just as much work and your
>>    simulations will be much slower.
>>
>>    -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
>>    <tel:%28540%29%20231-9080>
>>    http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>    <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >
>>
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>>
>> --
>> Best,
>> Liang Liu
>>
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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-- 
Best,
Liang Liu
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