[gmx-users] PLUMED plugin in gromacs for protein system

[neeru sharma]

Dear gromacs users,

I am a gromacs user and need some help regarding the implementation of
PLUMED plugin 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 came across the PLUMED plugin. I have some queries with respect to
the above matter.

1) Can we manually specify simulation length when performing the
simulation, that we want to finish the simulation in the given specified
time duration?
2) How can we specify reaction coordinates (Eg: The RMSD with the desired
output state, Specific H-bonding or distance pattern etc) for the
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).

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


Any help will be highly appreciated.

Thanks in advance

Regards,

Neeru
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