<div>With all due respect, this is clearly a RT*M moment.</div>
<div> </div>
<div>* = F</div>
<div> </div>
<div>Joao Henriques</div>
<div> </div>
<div>On Fri, Apr 15, 2011 at 1:03 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br></div>
<div class="gmail_quote">
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"><br><br>Monisha Hajra wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">Hi Justin,<br><br>I am trying to follow the protocol only.<br> More than the Gromacs own website, I find <a href="http://nmr.chem.uu.nl/~tsjerk/course/molmod/md.html#production" target="_blank">http://nmr.chem.uu.nl/~tsjerk/course/molmod/md.html#production</a> link is more useful.<br>
<br></blockquote><br>Clearly. This is one of many tutorials linked from the site I posted before.<br><br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">However, I am stuck at one step which is mentioned :<br><a href="http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis.html" target="_blank">http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis.html</a><br>
<br>I am not able to understand how to create traj.trr, traj.xtc and ener.edr file. Remaining all is self explained in the previous link.<br><br></blockquote><br>These files are output by mdrun, i.e. actually running a simulation.<br>
<br>-Justin<br><br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">Really appreciate any help.<br><br>Regards<br>Monisha<br><br><br>On Fri, Apr 15, 2011 at 8:06 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> Monisha Hajra wrote:<br><br> Hi User,<br><br> I have a protein which I have modeled by Homology modelling. The<br> modeled protein has no water molecules in its surrounding<br> environment.<br>
<br> How should I add water molecule so that I can start the<br> simulation process?<br><br><br> Please refer to the abundant tutorial material on the website:<br><br> <a href="http://www.gromacs.org/Documentation/Tutorials#General_GROMACS_Use" target="_blank">http://www.gromacs.org/Documentation/Tutorials#General_GROMACS_Use</a><br>
<a href="http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation" target="_blank">http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation</a><br><br> -Justin<br><br> Regards<br>
Monisha<br><br><br> -- ========================================<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>
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<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>
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