[gmx-users] How to explain the phenomenon of -genbox?

[Justin Lemkul]

On 4/18/14, 6:51 PM, maggin wrote:
> Hi,
>
> I use : genbox -cp box.6_newbox.gro -cs spc216.gro -o box.6_solv.pdb -p
> box.6.top
>
> Output configuration contains 301821 atoms in 100053 residues
> Volume                 :     3030.92 (nm^3)
> Density                :     1000.12 (g/l)
> Number of SOL molecules:  99801
>
> When I use VMD to see the structure of box.6_solv.pdb, it some strang, the
> picture is as follow,
>
> <http://gromacs.5086.x6.nabble.com/file/n5015927/%7BXRW%29NI8%40%29IN_6%5D%7BE%25K3D%40B.jpg>
>
> What I get from genbox is right?
>

That is literally the strangest thing I have ever seen from genbox.  You haven't 
performed any other manipulation on it?  It seems there are wildly distorted 
water molecules, which is something that genbox should never be able to produce.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
http://mackerell.umaryland.edu/~jalemkul

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