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 <jalem...@vt.edu
<mailto:jalem...@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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto: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>>
<mailto: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>
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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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========================================
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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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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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