[gmx-users] Free energy calculation

[Khadija Amine]

Could you please propound a suggestion more helpful for doing it?

Should I perform more MD simulation for my complexes?

*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​*
>>>
>>
>>
>