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 <[email protected]> wrote: > Hi, > > On Wed, Apr 4, 2018 at 9:26 PM Sanyam Kapoor <[email protected]> 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 <[email protected]> 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 <[email protected]> > 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 <[email protected]> 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 [email protected]. > > > > -- > > > > 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 [email protected]. > > > > > > > > > > > > > > > > -- > > > 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 [email protected]. > > > > > -- > > 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 [email protected]. > > > -- > 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 [email protected]. > -- 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 [email protected].
