[gmx-users] calculation of self energy of protein

[Justin Lemkul]

On 3/27/17 2:02 AM, Saumyak Mukherjee wrote:
> Dear Justin,
>
> Is there any way to get just the interaction energy between protein and
> water? In this case, the energy should not contain the self or inherent
> energy.
>

Set the protein and water as separate energygrps and extract the relevant 
nonbonded terms with gmx energy.

-Justin

> Thanks & regards,
> Saumyak
>
> On 27 March 2017 at 11:27, Saumyak Mukherjee <mukherjee.saumyak50 at gmail.com>
> wrote:
>
>> Thank you very much.
>>
>> On 27 March 2017 at 02:22, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>>
>>>
>>> On 3/26/17 4:49 PM, Saumyak Mukherjee wrote:
>>>
>>>> Dear Justin,
>>>>
>>>> Thanks for the reply.
>>>>
>>>> I have tried that already. I stripped out the protein trajectory using
>>>> trjconv, created an appropriate .tpr file using tpbconv (I am using
>>>> GROMACS
>>>> 4.5.6), and recalculated energy using mdrun -rerun.
>>>>
>>>> But does the resulting .edr file include only the inherent energy of the
>>>> protein or does it have information of the interaction energies with the
>>>> solvent as well? That precisely is the point I am confused about.
>>>>
>>>> I tried this with a protein in water system and also simulated a dry
>>>> protein separately to compare. The energies were way to different from
>>>> each
>>>> other. Does it mean that the solvent-protein interaction energies are
>>>> also
>>>> involved?
>>>>
>>>>
>>> If you have a protein-only trajectory and a protein-only .tpr file,
>>> there's no possible way for there to be any sort of protein-solvent
>>> interaction energy. The energies of a "wet" and "dry" protein system should
>>> be extremely different.
>>>
>>> -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
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>
>>
>>
>> --
>> ================================
>> *Saumyak Mukherjee*
>>
>> Junior Research Fellow
>> Prof. Biman Bagchi's Group
>> Solid State and Structural Chemistry Unit
>> Indian Institute of Science
>> Bangalore - 560012
>>
>> Mob : 8017292426
>> Alternative e-mail : saumyakmukherjee at gmail.com
>>                                 smukherjee at sscu.iisc.ernet.in
>> ================================
>>
>>
>>
>
>

-- 
==================================================

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

==================================================