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

[James Lord]

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?

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

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
Cheers
James

On Sun, Oct 19, 2014 at 2:05 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/18/14 8:51 AM, James Lord wrote:
>
>> Hi Justin,
>> Thanks for the prompt answer. I selected LJ-(SR) but I am getting a
>> positive fluctuating line over the simulation time. Looking at the vmd
>> movie I can see that protein (Lysozyme) is coming into contact with
>> surface
>> afte 10ns and is 5 nm away at the beginning?? my surface is a not charged
>> (polyethylene)?? I'd expect zero energy at beginning and upon touching the
>> surface negative value??? any comments? Sorry this has nothing to do with
>> Gromacs.
>>
>
> A few things:
>
> 1. Make sure your index groups are correctly constructed.
> 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.
> 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)
>
>
> -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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