[gmx-users] Re: LJ

Dr. Vitaly V. Chaban vvchaban at gmail.com
Fri Aug 26 22:13:20 CEST 2011

>Thank you so much for your explanation. I am just guessing in the last statement you meant *inter* molecular!

Yes. INTERmolecular, between chemically nonbonded particles.

>> 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.

Of course. These four are just an example for the most traditional
setup for periodic boxes with electrostatics.

>> 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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================

Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216

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