[gmx-users] Umbrella sampling's equilibration runs

James Starlight jmsstarlight at gmail.com
Tue Apr 30 19:38:17 CEST 2013


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 ?

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

Thanks for help,

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

> On 4/30/13 10:58 AM, James Starlight wrote:
>> Dear Gromacs users!
>> I have a question about umbrella sampling simulation based on the Justin's
>> tutorial.
>> According to the tutorial after definition of the set of conformers
>> extracted from the pulled trajectory I should run N equilibrating
>> simulations and N productions runs. In the tutorial I've found that all
>> equilibrations run in the NPT ensemble. In my case I have membrane
>> receptor
>> for each conformer extracted from the pulling trajectory I want to run 20
>> umbrella's simulations with different starting velocities in each case.
>> Should I re-equilibrate each conformer in the nvt+npt runs (re-assigning
>> velocities in the nvt run) or the velocities might be re-assigned in the
>> npt equilibrations ? What the time-prolongation of each equilibrations
>> should be for each conformer in case of membrane protein simulation?
> If you re-assign velocities to start NPT after NVT, what was the point of
> NVT? You destroy the previously established state.  Initialize velocities
> at the start of NVT, then preserve the ensemble information when moving to
> NPT, like any other simulation.
> The time frame is something you must decide based on your knowledge and
> observations of your system.  There is no definitive answer.
> -Justin
> --
> ==============================**==========
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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