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