[gmx-users] Protein-ligand

[RAHUL SURESH]

Thank you Justin

On Wed, Apr 19, 2017 at 6:23 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/19/17 8:40 AM, RAHUL SURESH wrote:
>
>> Dear Justin,
>> Thank you
>>
>> But What do you mean my appropriate energygrps.? Protein ligand.? Will
>> that
>> give interaction energy between ligand and protein.?
>>
>
> Yes.
>
> -Justin
>
>
> On Wed, 19 Apr 2017 at 5:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 4/19/17 6:50 AM, RAHUL SURESH wrote:
>>>
>>>> Dear Gromacs users
>>>>
>>>> how to determine the interaction energy between ligand and protein at
>>>>
>>> each
>>>
>>>> frame of simulation?
>>>>
>>>>
>>> Set appropriate energygrps in the .mdp file, create a new .tpr and use
>>> mdrun
>>> -rerun to recalculate the interaction energies from the existing
>>> trajectory.
>>> This quantity may or may not be physically meaningful, depending on the
>>> details
>>> of the force field.
>>>
>>> -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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> --
> ==================================================
>
> 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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> Gromacs Users mailing list
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*