Dear gromacs users,<br><br>I am a gromacs user and need some help regarding the implementation of flooding approach in gromacs.<br><br>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. <br>
<br>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.<br>
<br>1) Can we manually specify simulation length when performing
"Flooding simulation", that we want to finish the simulation in the
given specified time duration?<br>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).<br>3) How to set the parameter values for Eflnull, tau and deltaFO in flooding for a protein system ?<br><br>
<br>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? <br><br>Any help will be highly appreciated.<br>
<br>Regards,<br><br>Neeru Sharma<br>