Indeed :-)<br><br><br><div class="gmail_quote">2011/4/16 Joćo Henriques <span dir="ltr"><<a href="mailto:joao.henriques.32353@gmail.com">joao.henriques.32353@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<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><div class="h5">
<div> </div>
<div>On Fri, Apr 15, 2011 at 1:03 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br></div>
<div class="gmail_quote">
<blockquote style="border-left: 1px solid rgb(204, 204, 204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;" class="gmail_quote"><br><br>Monisha Hajra wrote:<br>
<blockquote style="border-left: 1px solid rgb(204, 204, 204); 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/%7Etsjerk/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: 1px solid rgb(204, 204, 204); 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/%7Etsjerk/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: 1px solid rgb(204, 204, 204); 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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<p style="margin-bottom: 0cm;" align="LEFT">======================================================================</p>
<p style="margin-bottom: 0cm;" align="LEFT">Thomas Evangelidis</p>
<p style="margin-bottom: 0cm;" align="LEFT">PhD student</p>
<p style="margin-bottom: 0cm;" align="LEFT">Biomedical Research
Foundation, Academy of Athens</p>
<p style="margin-bottom: 0cm;" align="LEFT">4 Soranou Ephessiou , 115 27
Athens, Greece<br><br>email: <a href="mailto:tevang@bioacademy.gr" target="_blank">tevang@bioacademy.gr</a></p>
<p style="margin-bottom: 0cm;" align="LEFT"> <a href="mailto:tevang3@gmail.com" target="_blank">tevang3@gmail.com</a></p>
<p style="margin-bottom: 0cm;" align="LEFT"><br>website:
<a href="https://sites.google.com/site/thomasevangelidishomepage/" target="_blank">https://sites.google.com/site/thomasevangelidishomepage/</a></p>
<p style="margin-bottom: 0cm;" align="LEFT"><br>
</p>
<br>