[gmx-users] Perturbing Proteins

Qasim Pars qasimpars at gmail.com
Tue Apr 3 23:15:54 CEST 2018


Good question! The nstcomm is the frequency at which the center of mass motion is removed. My guess is that using short frequency for the nstcomm (e.g. nstcomm=1 while simulation time step is 1 fs, dt=0.001) can perturbe the system. That is, the system may not return to its starting/unperturbed state within a short time interval, while nstcomm is applied at every step on the system. Maybe Justin, Mark or the other developers/users can comment it better than me.

> On 3 Apr 2018, at 23:53, 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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