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

[Justin Lemkul]

On 6/25/15 6:12 PM, Mahboobe Sadr wrote:
> I used spc water and the command was :
>
>   perl water_deletor.pl -in bilayer.gro -out bilayer_fix.gro -ref N4
> -middle C50 -water 3 -v yes
>

Using N4 as a reference is a bad idea; you don't want to desolvate the 
headgroups.  This will lead to unstable simulations.

Beyond that, I honestly don't know why it's producing weird behavior.  The 
script is really trivial; surely you can debug what's going on even with a few 
simple print statements.

-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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