[gmx-users] calculate potential with tabulated non-bonded interactions
Justin A. Lemkul
jalemkul at vt.edu
Thu Nov 17 17:06:27 CET 2011
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
> 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 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
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> Liang Liu
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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