[gmx-users] Umbrella sampling's equilibration runs

[Justin Lemkul]

On 4/30/13 1:38 PM, James Starlight wrote:
> Justin,
>
>
> could you also tell me
> 1) what difference should be expected from the umbrella sampling run with
> (as I want to do for better coverage) and without (as in your tutorial)
> velocities re-assignment on each umbrella window run ?
>

You have to discard more data at the outset of the production run.  Depending on 
the thermostat, initial forces may cause instability.  See previous discussions 
in the archive on this topic.

> 2) On what suggestions should I chose each conformer from pulling
> simulation for each umbrella run? If I have not reasonable kinetiks from
> the pulling simulation could I chose each conformer based on the RMSD from
> the starting structure (in some region- eg in active site) assuming that I
> investigate conformation motions in that region accompanied some functional
> transitions?
>

The establishment of the reaction coordinates and its component windows depends 
on what you're examining.  I can't tell you that.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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