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

[Justin A. Lemkul]

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://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
>     ==============================__==========
>     -- 
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/__mailman/listinfo/gmx-users
>     <http://lists.gromacs.org/mailman/listinfo/gmx-users>
>     Please search the archive at
>     http://www.gromacs.org/__Support/Mailing_Lists/Search
>     <http://www.gromacs.org/Support/Mailing_Lists/Search> before posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
>     <http://www.gromacs.org/Support/Mailing_Lists>
> 
> 
> 
> 
> -- 
> 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

========================================