<br>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.<br><div class="gmail_quote">On Wed, Dec 22, 2010 at 8:32 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><br>
<br>
sreelakshmi ramesh wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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.<br>
<br>
</blockquote>
<br></div>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
sree.<div class="im"><br>
<br>
On Tue, Dec 21, 2010 at 6:02 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
sreelakshmi ramesh wrote:<br>
<br>
can anyone tell me how to alter the parameter B OF buckingham<br>
potential.<br>
<br>
<br>
Manual, chapter 5, especially table 5.4, which specifically lists<br>
all of the parameters and where they are defined.<br>
<br>
-Justin<br>
<br>
regards,<br>
sree<br>
<br>
<br>
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Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
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jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
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========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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