Hi Neeru, Any number of enhanced sampling techniques might do this, but weighted ensemble, forward flux sampling, milestoning, and transition path sampling (all described in (Zwier, M. C.; Chong, L. T. Current Opinion in Pharmacology 2010, 10, 745–752.) and the nudged elastic band method (Bergonzo, C., Campbell, A.J., Walker, R.C., Simmerling, C., "A Partial Nudged Elastic Band Implementation for Use with Large or Explicitly Solvated Large Systems", Int. J. Quant. Chem., 2009, 109, 15, 3781-3790) come to mind. The nudged elastic band method, in particular, might be a good place to start, since you have initial and final structures.
To my knowledge, none of these is implemented directly within GROMACS, but all could be implemented using GROMACS as a dynamics backend. (NEB On Wed, Apr 18, 2012 at 2:26 AM, neeru sharma <[email protected]> wrote: > Dear Gromacs users, > > > I am simulating a system containing Protein-Mg-GDP and Protein-Mg-GTP using > Gromacs. I have already carried out classical MD simulation for the > Protein-Mg-GDP complex. Then, I replaced GDP with GTP in the complex and now > have to analyse the structural changes in the Protein-Mg-GTP complex during > the simulation. I tried to perform classical MD simulation for the > Protein-Mg-GTP complex too. But, as GDP to GTP state transition is a > millisecond time-scale event, through classical MD, it seems practically > impossible to achieve this time-scale transition. > > I already have the crystal structure available with me for the > Protein-Mg-GTP complex. > As, I am new to gromacs, can anybody suggest me any method to perform this > transition using some accelerated molecular dynamics method available with > gromacs and how it can be performed for my system? > > > Any help will be highly appreciated. > > Thanks in advance > > ----- > Neeru Sharma, > Pune (India) > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
