[gmx-users] How to calculate protein-surface interaction energy

[James Lord]

You are right it is the name of molecule type in .top, and thus no error
upon executing grompp, so index group is constructed correctly right???
rvdw=1 nm so should be fine. and for the last part I agree.
Cheers
James

On Sun, Oct 19, 2014 at 2:34 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/18/14 9:30 AM, James Lord wrote:
>
>> Hi Justin,
>>
>> 1. Make sure your index groups are correctly constructed.
>> Do I need to use make ndx? I thought just adding energygrps=protein
>> surface
>> at the end of .mdp is enough?
>>
>>
> "Surface" isn't likely a default group (unless that's the name of the
> [moleculetype]) and grompp should have raised a fatal error if the group
> wasn't defined.
>
>  2. What does 5 nm correspond to?  A COM distance?  A minimum distance?  If
>> the latter, then the LJ-SR energy should likely be zero, but if it's a COM
>> distance, that's not necessarily the case.
>> 5 nm is minimum distance
>>
>>
> OK, in this case, the initial LJ-SR should be zero, provided that rvdw < 5.
>
>  3. Is your PE model united-atom or all-atom?  If the latter, you still
>> have
>> partial charges that will contribute to a negative Coul-SR (of course,
>> this
>> is something you can check very simply
>> It is all atom
>>
>
> Then you must have partial charges on the individual atoms and therefore
> Coul-SR will be non-zero.
>
>
> -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
>
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