[gmx-users] Free energy calculation

[Justin Lemkul]

On 11/28/16 9:22 AM, Khadija Amine wrote:
> Could you please propound a suggestion more helpful for doing it?
>

MM/PBSA calculations use the MM energy and solvation free energy estimates from 
PB to give the free energy of a given conformation.  Combined with entropy 
calculations (Schlitter or quasi-harmonic approximation), you can get a decent 
estimate of the actual free energy.  The calculations neglect solvent, so if 
e.g. the solvent entropy is a significant contribution in a given system, the 
results may not be correct in an absolute sense, but for comparing point 
mutations, it's probably accurate enough.

> Should I perform more MD simulation for my complexes?
>

As with any MD result, you need good sampling and a converged ensemble.  A 
single simulation of 20 ns is neither.

-Justin

> *Khadija AMINE*
>
>
> *Computational Biology*
> *Postdoctoral Research Associate*
> *Carnegie Mellon University*
>
> On Mon, Nov 28, 2016 at 4:56 PM, Khadija Amine <kh.amine1 at gmail.com> wrote:
>
>> As I have mentioned in my first email, I want to calculate the free energy
>> of my protein-protein complex.
>>
>> I want to compute free energies for wild type and mutant complex and
>> compare them.
>>
>> *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

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