[gmx-users] Fwd: i want to use water_detetor.pl script

[Justin Lemkul]

On 6/14/15 2:37 AM, A. mohammadzadeh wrote:
> Hello dear users
>
> i want to  use  water_deletor.pl script to delete waters that has
> penetrated in lipid bilayer.How do i choose atom reference?
>

It depends on what your lipid is, and the choice is somewhat empirical. 
Hydration typically exists into the glycerol region, so waters deeper in the 
hydrophobic core should be deleted.  See usage info in the header of the script 
itself for an example for DPPC.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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