[gmx-users] LJ-14 energy

[Justin Lemkul]

On 7/15/15 8:39 PM, Ming Tang wrote:
> Dear Chaban and Justin,
>
>
>
> Sorry for the mis-action. Please ignore my last email.
>
>
>
> Thank you both for your free help.
>
> I am pulling a collagen triple helix in a periodic water box using umbrella
> direction-periodic. I want to calculate the Lennard-Jones 12-6 of the
> protein. According to Gromacs manual, it contains repulsive short-range term
> and attractive long-range term. Is the Lennard-Jones 12-6 energy simply the
> addition of LJ-SR and LJ-LR? I am interested in the energy trends more than

LJ-LR only exists with a twin-range cutoff approach.  The total LJ between any 
groups also includes LJ-14 for intramolecular terms.  Intermolecular LJ would be 
the sum of LJ-SR and LJ-LR, if the latter exists.

> the energy absolute values. So, if I can calculate the LJ 12-6 of the whole
> system, it is fine, because I can assume the energy of the water is not
> subject to change due to pulling.
>

Why can you assume that?  You're pulling a structure, which is a non-equilibrium 
process.  There will be different interactions as a function of time. 
Water-water interactions at long distance from the protein indeed are unlikely 
to be affected, but those close to the protein may be different (though 
electrostatics/hydrogen bonding are probably much more interesting). 
Water-protein interactions certainly can't be assumed to be unchanging during 
pulling.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================