[gmx-users] Perturbing Proteins

[Sanyam Kapoor]

Hi Mark,

I unfortunately don't have background in MD. Do you mind pointing me to
relevant literature? I can take over from there. I believe the key phrases
are "alternative configurations of a common topology" and "move sets". I
was planning to do MC style simulations but was worried that I might change
the topology to an exceptionally bad state.

Also, could you point me to places in Gromacs that can help me do this kind
of a thing?

On Wed, Apr 4, 2018 at 3:42 PM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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-- 
Regards,
Sanyam Kapoor
Masters in Computer Science
Courant Institute, New York University
https://www.sanyamkapoor.com