<br><br><div class="gmail_quote">On 26 August 2011 15:17, 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;">
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Juliette N. wrote:<div class="im"><br>
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On 26 August 2011 13:25, Dr. Vitaly V. Chaban <<a href="mailto:vvchaban@gmail.com" target="_blank">vvchaban@gmail.com</a> <mailto:<a href="mailto:vvchaban@gmail.com" target="_blank">vvchaban@gmail.com</a>>> wrote:<br>
<br>
>>. Now it is clear that<br>
>> the sum of [ LJ-14 + LJ (SR) ] give the actual non bonded<br>
potentials. Thank<br>
>> you so much.<br>
<br>
The answer actually depends on what you call "nonbonded potential". If<br>
you want to calculate e.g. the interaction energy between two<br>
molecules, then you should NOT include this term.<br>
<br>
<br>
Thank you for you reply. I am actually interested in interaction energies (cohesive energy between particles which is related to enthalpy of vaporization) and noticed that inclusion of this term results in far less accurate results. The net energy is of repulsion type and adding a positive term ( LJ-1-4) makes my results inaccurate. I am already using nexcl = 3 in the topology which means 1-5, 1-6 neighbors are accounted for. But still LJ -1-4 is appearing. So far I have been ignoring this term (energy value) in my calculations, but my concern is that by just neglecting this energy term (value) I am not ignoring the actual effect of a potential term on the physics of the system. Is there any way to switch off this term?<br>
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The term arises because nrexcl is set to 3. You should not adjust this value, as the force field was likely parameterized with this setting in mind and 1-4 interactions are calculated and scaled very specifically for certain reasons, not the least of which are dihedral interactions.<br>
<br>
Please keep in mind that (as I believe Mark recently said), you should not necessarily expect biomolecular force fields, which were designed to reproduce certain elements of protein dynamics (and sometimes other molecules), to necessarily reproduce the properties of any other material or other quantities. You may be finding simply a limitation of whatever force field you've chosen; it may not be suited to your task and you may end up having to design your own force field or modify an existing one. Though that can be an entire Ph.D. in itself...<br>
</blockquote><div><br>Thank you Justin. I am using OPLSAA which is suited for hydrocarbons and my system contains
only saturated hydrocarbon macromolecules. I hope I am
using the appropriate FF. I keep nrexcl to its default value but I am wondering if I can consider LJ SR (or coulomb SR) as the only nonbondd terms since the quantity I am looking at is cohesion between molecules. LJ 1-4 is to do with non bonded but intra molecular interactions which does not affect the interaction energies. Am I making ad hoc changes to the force field in this way or I am allowed to look for the terms (LJ SR or coulomb SR) according to the definition of the quantity I am after?<br>
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</div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><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">
Thanks,<br>
<br>
<br>
--<br>
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.<br>
Univ. Rochester, Rochester, New York 14627-0216<br>
THE UNITED STATES OF AMERICA<br>
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Thanks,<br>
J. N.<br>
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-- <br>
==============================<u></u>==========<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> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Thanks,<br>J. N.<br><br>