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 <jalem...@vt.edu
<mailto:jalem...@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://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
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