[gmx-users] Zero LJ energies during Free energy perturbation

[bipin singh]

Thank you Dr. Justin for your reply.


On Sat, Feb 8, 2014 at 3:12 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/7/14, 9:13 AM, bipin singh wrote:
>
>> Hello All,
>>
>> Using a B state topology in mdp file, I have switched off the vdw and
>> coulombic terms of a single atom in a molecule (H atom in CH3OH). I have
>> tried to see how the LJ energies (between CH3OH and solvent) changes
>> during
>> the transformation (from lambda=0 to lambda=1) but I get zero values at
>> both the lambda point (0 and 1) for both the LJ-SR and LJ-14 terms for
>> CH3OH and solvent LJ interaction.
>>
>>
> H atoms do not have LJ parameters in most force fields, so you will not
> see any changes.  LJ-14 are intramolecular and those interactions are going
> to all be excluded anyway in CH3OH, but again if an H is changing, there
> will be no difference in LJ energy.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 



*--------------------Thanks and Regards,Bipin Singh*