[gmx-users] Unexpected behavior in the output of gmx insert-molecules using the -ip option.

Justin Lemkul jalemkul at vt.edu
Wed May 31 02:09:00 CEST 2017

On 5/29/17 11:11 PM, Abhishek Acharya wrote:
> Dear GROMACS users,
> I want to insert my molecule of interest in a simulation box at specific
> positions, specified by a dat file.
> Now, when I run insert-molecules, I find that on "certain occasions" (yes,
> it doesn't happen always.), the program also inserts the molecule
> at the origin [0 0 0]. It seems that it is appending the input coordinates
> of my molecule, provided with -ci,
> to the final coordinate file, something which should not happen.
> Is this behavior known? Of course, it is trivial to remove the extra
> coordinates, but it becomes an effort if a large number of systems need to
> be
> generated.

Sounds buggy, but without an actual command and set of inputs that reliably 
triggers the behavior, it's hard to track down.  If you can provide that, please 
open a Redmine issue.



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


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