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

rama david ramadavidgroup at gmail.com
Mon May 28 22:09:20 CEST 2012

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???

Thank you in advance...

With Best Wishes,
Rama David.
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