[gmx-users] Perturbing Proteins

[Sanyam Kapoor]

Thanks Qasim and Joe!

@Joe
To be more specific, I am in search of valid topologies which are not yet
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.

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
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
>
> --
> Joe Jordan
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
-- 
Regards,
Sanyam Kapoor
Masters in Computer Science
Courant Institute, New York University
https://www.sanyamkapoor.com