[gmx-users] gmx insert-molecules

[Justin Lemkul]

On 6/7/17 1:20 PM, Li, Shi wrote:
> Dear GMX users,
> 
> I have a pure solvent system A with 100 molecules. Then I randomly removed
> 10 molecules out of the box, but keep the box size. Now I want to do a gmx
> insert-molecule to insert 10 molecule B into the system box. The problem is
> molecule B is slightly larger than molecule A. So in some cases, I couldn't
> insert the exact 10 molecules of B into the system. Is there a way to
> automatically adjust the size of the box according to the radius of
> molecule B, so that they can fit in? Or, is there a better solution to do
> this?
> 

Insert 10 of molecule B into an empty box, then solvate with a pre-equilibrated 
box of molecule A.  Works every time.

-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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