Hi Everybody, I am running MD simulation for getting various conformation of a molecule, that can act as better receptor for docking purpose. While doing so, I got a number of doubts. Firstly what should be the range of time step I can keep in .mdp file (right now I am using .002 ps of time step, Can I increase it further ?) My second question is for how long I should run my simulation to get various conformation (or what is the time interval that can be taken as in general after which biomolecule can change their conformation ?) How should I pick up various conformation from the mdrun that can make a sense ?
I know the questions are not strictly related to gromacs. my apologies for putting such questions. If anybody has insight into these questions, please reply. With Thanks, Vivek
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