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

Liu, Liang liu4gre at gmail.com
Thu Nov 17 17:04:35 CET 2011

Well, I already have the xvg files from others. However I don't know how to
use it.

On Thu, Nov 17, 2011 at 10:00 AM, Justin A. Lemkul <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
> 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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Liang Liu
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