[gmx-developers] Perturbing Proteins
sanyam at nyu.edu
Tue Apr 3 22:51:47 CEST 2018
Sorry about that!
On Tue, Apr 3, 2018 at 4:41 PM Mark Abraham <mark.j.abraham at gmail.com>
> 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.
> 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.
>> Sanyam Kapoor
>> Masters in Computer Science
>> Courant Institute, New York University
>> Gromacs Developers mailing list
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> * For (un)subscribe requests visit
>> or send a mail to gmx-developers-request at gromacs.org.
> Gromacs Developers mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> or send a mail to gmx-developers-request at gromacs.org.
Masters in Computer Science
Courant Institute, New York University
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-developers