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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