[gmx-users] Using gromacs for docking purpose

[vivek sharma]

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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