[gmx-users] Flooding approach and parameters for protein system

[neeru sharma]

Dear gromacs users,

I am a gromacs user and need some help regarding the implementation of
flooding approach in gromacs.

I am simulating a system containing Protein-Mg-GDP and Protein-Mg-GTP using
Gromacs which is a 166 residue protein+mg+GTP/GDP complex. 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 was looking for the methods available in gromacs that can accelerate this
event. I was reading a paper titled: " Flooding in GROMACS: Accelerated
Barrier Crossings in Molecular Dynamics". I have some queries with respect
to the above matter.

1) Can we manually specify simulation length when performing "Flooding
simulation", that we want to finish the simulation in the given specified
time duration?
2) Can we specify reaction coordinates (Eg: The RMSD with the desired
output state, Specific H-bonding or distance pattern etc) for the flooding
simulation, as I already have the crystal structure available with me for
the Protein-Mg-GTP complex (output state desired to be achieved with the
simulation).
3) How to set the parameter values for Eflnull, tau and deltaFO in flooding
for a protein system ?


As, I am new to gromacs, can you please help me regarding the above
mentioned matter and how it can be approached with my system?

Any help will be highly appreciated.

Regards,

Neeru Sharma
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