[gmx-users] Re: LJ

Justin A. Lemkul jalemkul at vt.edu
Fri Aug 26 22:07:27 CEST 2011

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.


> Vitaly
> On Fri, Aug 26, 2011 at 3:12 PM, Juliette N. <joojoojooon at gmail.com> wrote:
>> On 26 August 2011 13:25, Dr. Vitaly V. Chaban <vvchaban at 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
>>> --
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>> --
>> Thanks,
>> J. N.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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