[gmx-users] Methods for accelerated MD simulation for Protein-Mg-GTP system in gromacs

Matthew Zwier mczwier at gmail.com
Wed Apr 18 21:49:55 CEST 2012

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.

On Wed, Apr 18, 2012 at 2:26 AM, neeru sharma <neeru.bioinfo at gmail.com> 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)
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