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.
Mark
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