[gmx-users] Re: LJ

[Juliette N.]

On 26 August 2011 15:17, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Juliette N. wrote:
>
>
>>
>> On 26 August 2011 13:25, Dr. Vitaly V. Chaban <vvchaban at gmail.com<mailto:
>> 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?
>>
>>
> 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...
>

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?

 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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-- 
Thanks,
J. N.
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