[gmx-users] Re: Justin umbrella sampling tutorial......

Justin A. Lemkul jalemkul at vt.edu
Mon May 28 22:11:38 CEST 2012

On 5/28/12 4:09 PM, rama david wrote:
> Thank you Justin..
>         Is these alternative process is right or totally wrong..???
>     Using the checkpoint in this instance is wrong.  The only checkpoint you
>     have accessible to you at that point is from the end of the pulling
>     simulation and corresponds to the final state of the system.  Applying these
>     velocities to the intermediate configurations along the reaction coordinate
>     is likely to do weird and unreliable things to the trajectory.  It is more
>     robust to run NPT and then data collection, or as I said before, proceed
>     immediately to a continuous data collection (with gen_vel = yes!) and
>     discard the initial few ns of data as equilibration.  In theory, this
>     procedure is no different than any other simulation that one conducts.
> Check point file has velocity of the last co-ordinates and we are using middle
> configuration..
> Thank you for explaination ...
> I have another query..
> In npt equilibration can I use define = -DPOSRES (Position restrain all the
> protein along the chain B)
>   and in production md define = -DPOSRES_B ( Position restrain for chain B
> only..)  ???
> If not What is appropriate reason???

You can use either.  I have never tried it, but there is no reason to believe 
there will be any substantive reason during data collection.  The production MD 
period is significantly longer than the equilibration, and the results will 
likely turn out the same, when considering error estimates.  Sufficient sampling 
of any series of simulations should converge.



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


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