[gmx-users] Free energy calculation

[Justin Lemkul]

On 11/28/16 8:56 AM, Khadija Amine wrote:
> As I have mentioned in my first email, I want to calculate the free energy
> of my protein-protein complex.
>

That can be a bit ambiguous.

> I want to compute free energies for wild type and mutant complex and
> compare them.

This is a more clearly defined objective; presumably you want to do an MM/PBSA 
analysis.  I would not expect 20 ns to be nearly enough sampling, though.

-Justin

>
> *Khadija AMINE*
>
>
> *Computational Biology*
> *Postdoctoral Research Associate*
> *Carnegie Mellon University*
>
> On Mon, Nov 28, 2016 at 4:02 PM, Khadija Amine <kh.amine1 at gmail.com> wrote:
>
>> Thank you Williams.
>>
>> I should try the umbrella sampling tutorial?
>>
>> My complex is simulated during 20ns. The starting files for free energy
>> computing should be the MD production files?
>>
>>
>>
>> *Khadija AMINE*
>>
>>
>> *Computational Biology*
>> *Postdoctoral Research Associate*
>> *Carnegie Mellon University*
>>
>> On Mon, Nov 28, 2016 at 12:56 PM, Khadija Amine <kh.amine1 at gmail.com>
>> wrote:
>>
>>> Dear Gromacs users,
>>>
>>> I have a system of protein-protein interaction.
>>>
>>> Is it possible to calculate the free energy of the complex?
>>>
>>> If it so, could you please give me an efficient tool to compute the free
>>> energy calculation.
>>>
>>> Any suggestion. Thank you
>>>
>>>
>>> *Khadija AMINE*
>>>
>>>
>>> *Computational Biology*
>>> *Postdoctoral Research Associate*
>>> *Carnegie Mellon University​*
>>>
>>
>>

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

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

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