[gmx-users] buckingham potentials

[Justin A. Lemkul]

sreelakshmi ramesh wrote:
> 
> so if i set vdwtype =cut off and specify 2 in default section (2 is for 
> buck and 1 for LJ ) of topology file will gromacs makes suer that i want 
> the calculation with bucking ham potential.

Presumably, since that's what the manual would indicate works.  You can answer 
these sorts of questions yourself by giving it a try, then verifying the run 
parameters by using gmxdump on the resulting .tpr file.

-Justin

> On Wed, Dec 22, 2010 at 8:32 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     sreelakshmi ramesh wrote:
> 
>         Thanks a lot for timely reply by gmxusers.I read the manual and
>         i had altered the buckingham coefficients in topolgy file.Now in
>         mdp file in vdwtype i want to specify it as buckingham but looks
>         like i can mention only LJ and in manual they haven't told about
>         the notation for BJ.any suggestions please.
> 
> 
>     Use of Buckingham potentials is not controlled by the .mdp file,
>     except in the fact that several of the vdwtype methods cannot be
>     used in conjunction with Buckingham (see manual, section 7.3.11);
>     only "cutoff" appears to be viable here.
> 
>     -Justin
> 
> 
>         sree.
> 
> 
>         On Tue, Dec 21, 2010 at 6:02 PM, Justin A. Lemkul
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
> 
> 
> 
>            sreelakshmi ramesh wrote:
> 
>                can anyone tell me how to alter the parameter B OF buckingham
>                potential.
> 
> 
>            Manual, chapter 5, especially table 5.4, which specifically lists
>            all of the parameters and where they are defined.
> 
>            -Justin
> 
>                regards,
>                sree
> 
> 
>            --     ========================================
> 
>            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

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