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<div class="gmail_quote">On Tue, Oct 18, 2011 at 11:41 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"><br><br>Steven Neumann wrote:
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<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"><br><br>On Mon, Oct 17, 2011 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> Steven Neumann wrote:<br><br> Dear Gmx Users,<br> I would like to calculate the interaction energy (LJ and<br> electrostatic) between each residue and my ligands (10 ligands<br> in the system). I would like to see what is the contribution of<br>
electrostatic and vdW interactions between ligand and each of my<br> residue. I thought to use g_energy and specify each of my<br> residues in index files but it is not possible. Will you suggest<br> how to do this?<br>
<br><br> For such information, you have to specify these groups as energygrps<br> in the .mdp file. You can rerun the trajectory using mdrun -rerun<br> and a new .tpr file specifying these groups, but depending on the<br>
output frequency, the result may not be as accurate as you'd like.<br><br> -Justin<br><br> Thank you Justin. Now I have two groups sepcified in my mdp file:<br> energygrps = Protein LIG<br><br>How can I specify each residue of my protein separately and each ligand? In my md.gro file I have residues:<br>
<br> 91GLY 92TYR ..... 161LIG 162LIG...<br><br> Will it be correct like this<br> energygrps = 91GLY 92 TYR ... 161LIG 162LIG...<br> <br></blockquote><br></div></div>No. The names must correspond to valid groups in an index file.
<div class="im"><br></div></blockquote>
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<div>So do you mean that that I should add my index file with</div>
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<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="COLOR: #3366ff; mso-ansi-language: PL" lang="PL"><font size="3"><font face="Times New Roman">grompp -f md.mdp -c npt.gro -n <strong>index.ndx</strong> -t npt.cpt -p topol.top -o md.tpr</font></font></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="COLOR: #3366ff; mso-ansi-language: PL" lang="PL"><font size="3" face="Times New Roman"></font></span> </p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal">with specified groups in md.mdp file like they are specified in index file? :) Then just to</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"> </p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal">mdrun -rerun -deffnm md2</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"> </p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal">Please, let me know whether I am correct or not.</p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"> </p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal">Steven</p></div>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div class="im"><br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">If yes, will this simulation take longer? Thank you<br></blockquote><br></div>Perhaps, but certainly your energy file will be considerably larger.<br>
<br>-Justin<br><br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"> Steven<br><br> <br> <br></blockquote>
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<div class="h5"><br>-- <br>==============================<u></u>==========<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> | <a href="tel:%28540%29%20231-9080" target="_blank" value="+15402319080">(540) 231-9080</a><br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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