[gmx-users] Using gromacs for docking purpose

[vivek sharma]

Hi Justin,
Thank you very much for your quick reply.... It is really encouraging to get
such response
For the answer of third question, How can I assign different random velocity
?
Is it like assigning the different force-field ?
Please elaborate or suggest some reference if you can ?


With Thanks,
Vivek

2008/9/10 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> 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 :)
>
> -Justin
>
>  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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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