One last question! <br><br>1- So what are the 12 energy terms I get by passing index file onto step 2 below? I ignored rerun! what does rerun does?<br>
<br><br>2- So I dont have to include index file in mdrun initially..In brief what I need is:<br><br><br>
step 1 grompp .....(no index)<br>
<p class="PreformattedText" style="text-align: justify;"><span lang="EN-US"> step 2 mdrun -s old.tpr -o old.trr -c *.gro</span></p><p class="PreformattedText" style="text-align: justify;">(grompp and mdrun as usual) then:<br>
</p>
<p class="PreformattedText" style="text-align: justify;"><span lang="EN-US"> grompp -f energygroups.mdp -c .top -o new.tpr <b> -n index.ndx</b><br>
</span></p>
mdrun <b>-s new.tpr -rerun old.trr...</b><br><br><br>Please confirm. Many thanks for your help.<br><br><br><br><br><div class="gmail_quote">On 22 February 2011 17:35, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<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;">
<br>
Dear Justin,<br>
<br>
Thanks for your reply and Sorry for asking naive questions...<br></blockquote></div></blockquote><div><br><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;">
<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>
</blockquote>
<br></div>
If you don't want your energies on a per-chain basis, then yes.<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- 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>
</blockquote>
<br></div>
You need to create a new .tpr file that has the desired groups specified in it. You pass the new .tpr file to mdrun, in conjunction with your old trajectory (i.e., mdrun -s new.tpr -rerun old.trr).<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- 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>
</blockquote>
<br></div>
Sign matters a lot. Positive is repulsive, negative is attractive. You can't just switch them arbitrarily.<br>
<br>
-Justin<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><div></div><div class="h5">
Thanks,<br>
<br>
<br>
<br>
Nick wrote:<br>
<br>
Dear experts,<br>
<br>
1- I am trying to get interaction energies between solute (3<br>
chains A) and solvent 50 molecules B. In the index file I<br>
created two groups: one for all atoms of [A] and and [B] for all<br>
solvent molecules. and by setting A and B as energy groups in<br>
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<br>
different groups for my solute to get interaction energies A-A,<br>
A-B and B-B. I mean do I need to have [A1] for solute chain 1<br>
...[A3] for chain 3?<br>
<br>
<br>
If you want a breakdown of per-chain energetics, then yes, specify<br>
each chain as a group. The programs will only do what you tell<br>
them, nothing more, nothing less.<br>
<br>
<br>
<br>
<br>
and then sent A1, A2, A3 in mdp file and run g_energy? if I need<br>
to specify different chains, then to get say A-A should I<br>
average over all possible A1-A2, A1A3, A2-A3, A1-B, A2,B...? I<br>
am really confused ..<br>
<br>
<br>
Theoretically, the short-range terms should sum, not average.<br>
<br>
<br>
2- I know it is naive question but What does A1-A1 mean? How can<br>
one chain interact with itself?<br>
<br>
<br>
Without knowing what the chain is, no one can answer this.<br>
Generally, any atoms that are within the short-range cutoff and<br>
further away than nrexcl bonds contribute to short-range<br>
interactions. Long-range interactions (i.e., PME terms) happen too,<br>
but you can't decompose that term with energygrps.<br>
<br>
<br>
3- Do I need to use mdrun - rerun option to get beakdown or just<br>
g_energy gives what I need?<br>
<br>
<br>
You need to -rerun. g_energy does not take an index file, and it<br>
only analyzes existing groups, it cannot derive new ones.<br>
<br>
-Justin<br>
<br>
<br>
Thanks for your help<br>
Paniz<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>
Blacksburg, VA<br></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><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>
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<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>
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>
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