Juliette N. wrote:
On 26 August 2011 13:25, Dr. Vitaly V. Chaban <vvcha...@gmail.com
<mailto:vvcha...@gmail.com>> wrote:
>>. Now it is clear that
>> the sum of [ LJ-14 + LJ (SR) ] give the actual non bonded
potentials. Thank
>> you so much.
The answer actually depends on what you call "nonbonded potential". If
you want to calculate e.g. the interaction energy between two
molecules, then you should NOT include this term.
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?
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.
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...
-Justin
Thanks,
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
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Thanks,
J. N.
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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