On Fri, Jan 27, 2012 at 12:22 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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Naomi Fox wrote:<div><div></div><div class="h5"><br>
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On Thu, Jan 26, 2012 at 7:20 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.<u></u>au</a>>> wrote:<br>
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On 27/01/2012 12:35 PM, Naomi Fox wrote:<br>
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I would like to print out a list of non-bonded interactions and<br>
their associated LJ-potentials and coulombic potentials.<br>
<br>
I tried g_energy, but couldn't figure out the combination of<br>
parameters to get this information.<br>
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<br>
During the simulation, you can only save the magnitude of the<br>
interactions between energy groups (see manual), and by default the<br>
only such group is the whole system. mdrun -rerun is useful for<br>
re-computing quantities based on an existing simulation.<br>
<br>
Mark<br>
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So what you're saying is it isn't possible? <br>
When I rerun mdrun with the -seppot option, I see in the md.log file that I get the VdW and Coulomb V and dVdl for node 0 (the only node).<br>
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There is no way to print the exact contribution from each individual interaction?<br>
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It certainly is possible, you just need to specify energygrps (in the .mdp file) for the interactions you want to monitor, as Mark said. The -seppot flag is for the free energy code, IIRC, not a magic option to dump a bunch of different interactions.<br>
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-Justin<br>
<br></blockquote><div><br></div><div>Thanks Mark and Justin.</div><div><br></div><div>Two more questions:</div><div><br></div><div>1) How do I define an energy group for an interaction? All I found for examples in the manual are "Protein" and "SOL"</div>
<div><br></div><div>2) Can I dump all the interactions listed as [ pairs ] in the .top file? I only need them for a single conformation and not for a full trajectory. </div></div>