[gmx-developers] Perturbing Proteins

[Sanyam Kapoor]

Sorry about that!

On Tue, Apr 3, 2018 at 4:41 PM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> These are good questions for the gmx-users mailing list. On this list we
> discuss issues pertaining to the code, rather than the use of the code.
> Thanks!
>
> Mark
>
> On Tue, Apr 3, 2018 at 10:26 PM Sanyam Kapoor <sanyam at nyu.edu> wrote:
>
>> Hi all,
>>
>> I was wondering if there is a principled way to perturb molecules and
>> then see its energy converge to the stationary state via the simulation.
>> Perturbation could mean changing the coordinates of the atoms, changing
>> angles dihedrals etc. Anything related to the topology. I want to see this
>> without the addition of any solvents in the environment.
>>
>> My concern is that if I perturb randomly, the molecule may no more remain
>> in a valid state (bad bond distance or bad angles/dihedrals etc.). Any
>> ideas here?
>>
>> Another question is that if I pick up any molecule from Protein DataBank
>> and run a simulation without any solvent addition, does it converge further
>> or are those molecules already on some minimum energy value attainable?
>>
>> Please correct me if I miss some part of the molecular dynamics pipeline.
>> --
>> Regards,
>> Sanyam Kapoor
>> Masters in Computer Science
>> Courant Institute, New York University
>> https://www.sanyamkapoor.com
>>
> --
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-- 
Regards,
Sanyam Kapoor
Masters in Computer Science
Courant Institute, New York University
https://www.sanyamkapoor.com
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