<div>Dear Justin,</div>
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<div>I want to get energy per residue not time. if i use mdrun -rerun with energygrps in md.mdp then g_energy i obtain enery per time not residue.<br clear="all">at last, i don't understand how to get Energy per residue .</div>
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<div><br>Best wishes, <br>Afsaneh </div><br><br>
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<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div class="im">afsaneh maleki wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">Dear gromacs users,<br> Is there a way to get energy values (Vdw,..) per residue at the end of MD prosses?<br>
<br></blockquote><br></div>Yes and no. You won't be able to get, for instance, the absolute van der Waals energy of a residue. That doesn't really make any sense, since vdW interactions take place between particles. There may be some 1-4 type interactions within a residue that you could quantify, but not much else.<br>
<br>You can decompose short-range residue-residue energies using energygrps in the .mdp file, and re-running the trajectory with the new .tpr file (mdrun -rerun), but the .edr file can quickly get out of hand in terms of disk usage, depending on how many groups you have (since you will then have essentially N^2 energy terms to write out, where N is the number of energygrps).<br>
<br>-Justin
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<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"> I would really appreciate any help.<br><br>Afsaneh<br><br></blockquote><br></div>-- <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>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><br></blockquote></div>