[gmx-users] buckingham potentials
Justin A. Lemkul
jalemkul at vt.edu
Wed Dec 22 04:53:13 CET 2010
sreelakshmi ramesh wrote:
> I am using gromos force field fotr my work and This force field's files come filled
> with LJ functions and now if i want to work with buckingham potential i changed in
> default section of force field ffG34a21.itp file but it gives me the follwing errors
>
>
> ERROR 77 [file ffgmxnb.itp, line 144]:
> Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR)
>
You can't simply hack a force field into using a different nonbonded function
type. To do so, you'd have to re-write the whole force field. None of the
common biomolecular force fields use Buckingham.
-Justin
> any help appreciated.
>
>
> On Wed, Dec 22, 2010 at 8:40 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> 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>
> <mailto: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>>
> <mailto: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>
> <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> <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
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