[gmx-users] Expanding of the boundaries of the enssemble

[Justin Lemkul]

On Thu, Nov 21, 2013 at 12:06 PM, James Starlight <jmsstarlight at gmail.com>wrote:

> Mark, does it possible to do such for the ensemble (each frame from the
> trajectory) at one step ? For example I need to perform umbrella sampling
> in 50 windows extracted from the initial trajectory expanding in each
> umbrella window the Z dimension and add water to it.
>
>
I can't think of any way to do this in one step, but it's trivial to
script. There is no getting around the fact that you need to perform
multiple manipulations on multiple configurations. Keep in mind that the
resulting structures may not be topologically identical (number of waters
may vary) so you will need a corresponding topology for each configuration,
anyway.

-Justin

-- 

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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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