<pre>I am using gromos force field fotr my work and This force field's files come filled<br> with LJ functions and now if i want to work with buckingham potential i changed in <br>default section of force field ffG34a21.itp file but it gives me the follwing errors<br>
<br></pre><pre style="margin: 0em;">ERROR 77 [file ffgmxnb.itp, line 144]:<br> Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR)<br><br>any help appreciated.<br></pre><br><div class="gmail_quote">On Wed, Dec 22, 2010 at 8:40 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;">
<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>
</blockquote>
<br></div>
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.<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;"><div class="im">
On Wed, Dec 22, 2010 at 8:32 AM, 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>
Thanks a lot for timely reply by gmxusers.I read the manual and<br>
i had altered the buckingham coefficients in topolgy file.Now in<br>
mdp file in vdwtype i want to specify it as buckingham but looks<br>
like i can mention only LJ and in manual they haven't told about<br>
the notation for BJ.any suggestions please.<br>
<br>
<br>
Use of Buckingham potentials is not controlled by the .mdp file,<br>
except in the fact that several of the vdwtype methods cannot be<br>
used in conjunction with Buckingham (see manual, section 7.3.11);<br>
only "cutoff" appears to be viable here.<br>
<br>
-Justin<br>
<br>
<br>
sree.<br>
<br>
<br>
On Tue, Dec 21, 2010 at 6:02 PM, Justin A. Lemkul<br>
<<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>><br></div><div class="im">
<mailto:<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>
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ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
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Virginia Tech<br>
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Justin A. Lemkul<br>
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ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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