[gmx-users] Perturbing Proteins

Joe Jordan e.jjordan12 at gmail.com
Wed Apr 4 08:43:19 CEST 2018


There are a number of ways to bias a system. Many of them are implemented
in gromacs. You will need to be more specific about what you want here.

The structures you find in the PDB are in an energy minima but these (lets
call them physical) minima may not be (lets call them theoretical) minima
of the force field you chose.

On Tue, Apr 3, 2018 at 11:15 PM, Qasim Pars <qasimpars at gmail.com> wrote:

> Hi,
>
> 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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-- 
Joe Jordan


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