<br><div class="gmail_quote">Dear Justin,<br><br>Thanks for your reply and Sorry for asking naive questions... <br><br>1- I am looking at all possible interaction energies between components A and B. that is A-A AB and BB. So interaction between single chains is not what I want. With this I think my initial approach was right. That is putting all atoms of 3 A chains under [A] and the same all solvent atoms under [B] and setting A and B as energy groups in mdp. Am I right?<br>
<br>2- One more thing bout question 3: I am passing on index.ndx to mdrun command. <br><br>with the index file I talked about I am getting the follwoing for AA AB and BB: LJ SR, LJ 1-4 coulomb SR and 1-4. (i.e 12 energy terms). <br>
<br>I think you say I need rerun since you assumed I did not pass it onto mdrun. right?<br><br>3- to get intermolecular interaction energies say for AA I need to add up LJ SR+coulomb SR? say +123-50=73 ? or just take absolute values : 123+50=173 ?<br>
<br>Thanks,<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"><br>
<br>
Nick wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear experts,<br>
<br>
1- I am trying to get interaction energies between solute (3 chains A) and solvent 50 molecules B. In the index file I created two groups: one for all atoms of [A] and and [B] for all solvent molecules. and by setting A and B as energy groups in mdp file I am getting break down as A-A, A-B and B-B with g_energy.<br>
<br>
I am a little confused as I dont know if I need to create different groups for my solute to get interaction energies A-A, A-B and B-B. I mean do I need to have [A1] for solute chain 1 ...[A3] for chain 3?<br>
<br>
</blockquote>
<br></div>
If you want a breakdown of per-chain energetics, then yes, specify each chain as a group. The programs will only do what you tell them, nothing more, nothing less.<div class="im"><br>
<br></div></blockquote><div><br> </div><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">
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
and then sent A1, A2, A3 in mdp file and run g_energy? if I need to specify different chains, then to get say A-A should I average over all possible A1-A2, A1A3, A2-A3, A1-B, A2,B...? I am really confused ..<br>
<br>
</blockquote>
<br></div>
Theoretically, the short-range terms should sum, not average.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
2- I know it is naive question but What does A1-A1 mean? How can one chain interact with itself?<br>
<br>
</blockquote>
<br></div>
Without knowing what the chain is, no one can answer this. Generally, any atoms that are within the short-range cutoff and further away than nrexcl bonds contribute to short-range interactions. Long-range interactions (i.e., PME terms) happen too, but you can't decompose that term with energygrps.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
3- Do I need to use mdrun - rerun option to get beakdown or just g_energy gives what I need?<br>
<br>
</blockquote>
<br></div>
You need to -rerun. g_energy does not take an index file, and it only analyzes existing groups, it cannot derive new ones.<br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thanks for your help<br>
Paniz<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>
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