[gmx-users] Perturbing Proteins

[Mark Abraham]

Hi,

On Wed, Apr 4, 2018 at 9:26 PM Sanyam Kapoor <sanyam at nyu.edu> wrote:

> Thanks Qasim and Joe!
>
> @Joe
> To be more specific, I am in search of valid topologies which are not yet
>

Generally we refer to those as alternative configurations of a common
topology.

at the energy minima. Since, manually building/generating them would be
> impractical, I thought if I could take a topology which has achieved its
> energy minima and do a valid "perturbation", I could then have many such
> valid topologies which exhibit non-stationarity.
>

Monte Carlo style simulations of such systems generate plausible
alternative configurations from many different kinds of move sets (see
literature). Of course many moves would be to a highly non-physical state,
which you would accept only with extremely low  probability, and
essentially all of them will lack stationarity (even though there are very
many stationary points, they are only a tiny part of the phase space).

Mark

On Wed, Apr 4, 2018 at 2:43 AM Joe Jordan <e.jjordan12 at gmail.com> wrote:
>
> > 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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> --
> Regards,
> Sanyam Kapoor
> Masters in Computer Science
> Courant Institute, New York University
> https://www.sanyamkapoor.com
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