Hello Mark,<br><br>Thank you for your reply. I have already created the energy groups. I am
trying to validate pairwise energy values (nonbonded) with some other
work ( a thermodynamic model) where they fit these AA AB BB (E_AA, E_AB, E_BB) energies so
that some phase diagrams are reproduced. The pairwise energies defined in the
model are in KJ/mol. <br>
<br>
Since my energies are not per mol, my results are useless,
unfortunately. As they depend on number of molecules in the system. To
achieve my goal, what do you suggest? For a binary system, can I run two
separate simulations for pure A and B in which case using -nmol gives
per mol energies and somehow predict AB from them? Does this make sense?<br>
<br>
Please guide me, I am stuck on this..<br>
<br>
Thanks,<br><br><div class="gmail_quote">On 9 April 2011 20:56, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</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><div></div><div class="h5">On 8/04/2011 12:18 PM, Elisabeth wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hello everyone,<br>
<br>
I have encountered a simple problem. For a homogenous system what g_energy reports is dependent on the system size and one needs to use -nmol option to divide energies by number of molecules to obtain per mol values.<br>
<br>
I am attempting to extract interaction energies between species in a three component system. I am puzzled how this can be achieved for such a system. Say there are 100 solvent, 20 solute A and 10 B molecules.<br>
</blockquote>
<br></div></div>
You would have to start by defining energy groups that contain relevant sets of molecules (see manual). Even once you've got them, the group-wise energies won't mean much of anything. Every observable is dependent on the configuration microstate, and unless you can estimate the relative population of different microstates to estimate a free energy...<br>
<br>
Mark<br><font color="#888888">
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