Dr. Vitaly V. Chaban wrote:
Hi Juliette,
Formally, you can kill this energy by going to the main topology file
(like ffgmx.itp) and setting FudgeLJ term to zero, although I think
that you don't actually want to do so. LJ-14 is the energy between the
atoms belonging to the SAME molecule, so if you consider e.g. heat of
vaporization, cohesive energy density, internal energy (U), you can
just ignore this term.
If I recollect correctly, nexcl and 1-4 interactions work
independently. "nexcl" requests to treat the atoms as if they belong
to separate molecules provided that these two atoms are separated by
more than a specified number of chemical bonds. 1-4 interactions only
treat 1-4 atoms using a scaling factor from FudgeLJ (above).
When calculating some intramolecular property, you usually need to use
only the following terms
I assume you mean intermolecular here?
LJ-(SR) Disper.-corr. Coulomb-(SR) Coul.-recip.
There may be others, depending on the way in which the .mdp file was set,
including LR terms for both LJ and Coulomb. The PME term is not trivially
decomposed, but that's been discussed to death in previous messages. There may
be other terms if PME was not used.
-Justin
Vitaly
On Fri, Aug 26, 2011 at 3:12 PM, Juliette N. <joojoojo...@gmail.com> wrote:
On 26 August 2011 13:25, Dr. Vitaly V. Chaban <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?
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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