[gmx-users] TFE-water simulation

[Justin Lemkul]

On 10/23/13 7:20 AM, Archana Sonawani-Jagtap wrote:
> Hi all,
>
> I have never performed TFE-water simulation therfore I want to know after
> inserting the peptide in the pre-equilibrated TFE-water mixture, do we need
> to adjust the number of TFE or water molecules ?
>

That depends on how you constructed the system.  genbox will not automatically 
update the number of TFE, but it can update the number of water molecules if you 
chose the proper command-line option.  Regardless, the [molecules] section of 
the .top must accurately reflect the contents of the configuration in terms of 
order and number of molecules.  Simple grep statements will let you count how 
many of each are present.

-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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