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

neeru sharma neeru.bioinfo at gmail.com
Wed Apr 18 08:26:35 CEST 2012

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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