[gmx-users] Potential Tables for user defined potentials

[Justin A. Lemkul]

Gareth Tribello wrote:
> Hello again
> 
> OK I have posted my notes on user defined potnetials here.  I think 
> there pretty exaustive (well they have everything I know about this in) 
> and could be used as a how to in this form.  However, I can't work out 
> how to post them on the webiste as a how to page.
> 

Great, I'll try to find some time to get a How-To together and post this file as 
an attachment.  I'll report back when that's done so others can add to it.

-Justin

> Gareth
> 
>      
> 
> On Sun, Apr 4, 2010 at 9:22 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Gareth Tribello wrote:
> 
>         Hi all
> 
>         I have just been stuck on this very problem of user defined
>         potentials.  When I emailed this list I was asked if I could
>         make notes on the solution as this is a problem that seems to
>         come up a lot.  Anyway, I will send the notes to you separately
>         Sikandar and would ask if anyone knows where should put/send
>         them if they are to be accessible to the user community?
> 
> 
>     Yes, please post whatever pointers  you have to the list so it can
>     be archived, and if you have time, create a How-To page on the
>     Gromacs site.  In recent weeks, it seems that half of the questions
>     asked are in regards to tabulated potentials.  It would be nice to
>     have some help information accessible.
> 
>     -Justin
> 
> 
>         Many thanks
>         Gareth
> 
> 
>         On Sun, Apr 4, 2010 at 3:47 AM, Justin A. Lemkul
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
> 
> 
> 
>            Sikandar Mashayak wrote:
> 
>                Hi
> 
>                I plan to do 'fluid in channel' simulations using GROMACS
>         4.0.7.
>                For that I need to use custom potential field parameters for
>                fluid-fluid and fluid-wall interactions.
> 
>                So my question is that, how can I use potential table
>         approach
>                to specify fluid-fluid and fluid-wall interactions
>         seperately?
> 
> 
>            Start with the manual, section 6.7.2, and see the table*.xvg
>         in the
>            /share/top subdirectory of your Gromacs installation for
>         examples.
> 
>            -Justin
> 
>                Thanks
>                sikandar
> 
> 
>            --     ========================================
> 
>            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> <http://vt.edu> | (540)
>         231-9080
> 
>            http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 
>     -- 
>     ========================================
> 
>     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
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 

-- 
========================================

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

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