[gmx-users] Using gromacs for docking purpose

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 10 14:53:52 CEST 2008

vivek sharma wrote:
> 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 ?)

That depends largely on your force field and whether or not you're applying 
constraints.  For protein simulations (with constraints), 1-2 fs is pretty 
standard; some UA lipid simulations use 4-5 fs.

> 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 ?)

There is no simple answer to this question.  Sampling is always an issue in MD. 
  Some conformational changes occur on the nanosecond timescale, others in 
excess of several hundred ns, or even a few microseconds!  Perhaps your system 
alters its conformation rapidly, such that changes can be observed in a few ns, 
but that is for you to determine :)

> How should I pick up various conformation from the mdrun that can make a 
> sense ?

Probably the best idea (IMHO) is to run several simulations, each starting from 
different random velocities.  Run each for the same length of time and compare 
the results.  Do all the simulations wind up giving you the same thing?  Are 
there substantial differences in the conformations?

As for extracting conformations along a trajectory (using trjconv -dump), this 
may or may not be relevant.  What if a certain conformation occurs once for a 
single frame in one trajectory, but never again in ten other trajectories?  Do 
you care about that frame?  Probably not, based on reasonable sampling.  What if 
a certain conformation occurs a few times over a few trajectories?  How do you 
determine its relevance?  Such are the challenges of simulation.

You can use g_cluster to do RMSD clustering to determine which conformations are 
similar along the trajectory.  Whether or not any of these "make sense" is 
entirely up to you and what you know about your system :)


> 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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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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