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

[James Lord]

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.
Cheers
James


On Sat, Oct 18, 2014 at 11:48 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/18/14 6:45 AM, James Lord wrote:
>
>> Dear Justin & Diogo,
>> Thanks for your comments, I did the steps you guys mentioned to calculate
>> protein-suface interaction energy and expect to see "protein surface"
>> option upon running g_energy but it is not the case, any comments? Here is
>> what I did,
>> gedit md.mdp and then added at the end of md.mdp file
>> energygrps= protein surface
>> saved it and
>> grompp -f md.mdp -c  mdw.gro -t mdw.cpt -p toplgy.top -o mdnew
>> mdrun -s mdnew.tpr -rerun mdw.xtc
>>
>> g_energy -f mdnew.edr -o energy.xvg
>>
>>
> You will not see a single energy term; rather you will see both LJ and
> Coulombic terms like LJ-SR(Protein:Surface).
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
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> University of Maryland, Baltimore
> 20 Penn St.
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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