[gmx-users] Umbrella sampling's equilibration runs

[James Starlight]

Couple extra question about umbrella

Does it possible to use Collective variable (eigenvector from EDA or NMA)
as the pulling coordinate?
Does it possible to use output from essential dynamics sampling (here I can
use EDS in targeted mode to pull my structure to the target conformation)
for the umbrella's NPT+MD. What the input data in the mdp files must be in
that case using CV?

James

2013/4/30 Justin Lemkul <jalemkul at vt.edu>

>
>
> 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
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