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

Mark Abraham Mark.Abraham at anu.edu.au
Wed Apr 18 09:04:58 CEST 2012

On 18/04/2012 4:26 PM, neeru sharma 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?

Defining GDP, GTP and what you wish to observe during the transition is 
going to be necessary information for anyone to be able to help you.


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