[gmx-users] gmx insert_molecules problem

Justin Lemkul jalemkul at vt.edu
Tue Apr 4 14:57:18 CEST 2017

On 4/4/17 2:42 AM, 吴萌 wrote:
> Hi All,
>   I am running a membrane protein MD simulation with Gromacs 5.1.4. I want to add some substrate molecules(acetate) to my system, and I used this command:
>   "gmx insert_molecules -f ###.pdb(include the ptotein, POPC, etc.) -ci act.pdb -o ###.pdb -nmol 48 -box 6.7 6.7 8.1 -try 500 -rot xyz",
>   but then I found many acetate molecules are put out of the system in the out .pdb.
>   Is that normol or wouldl affect the later MD process? If so, how can I fix it.
>   Any suggestions would be greatly appreciated. Thank you in advance!

There's no such thing as "outside" of a periodic box.



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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