[gmx-users] how to remove some molecules

[Justin Lemkul]

On 7/23/13 5:40 AM, niaz poorgholami wrote:
> Dear gmx-users
> I would like to calculate the PMF in a system composed of
> nanotube+surfactants. for doing this I use the final configuration of
> previous surfactant adsorption simulation onto carbon nanotube. the problem
> is I want to remove some of  non-adsorbed surfactant molecules. Would you
> please help me how I can do that? any help would be highly appreciated.
>

Delete them from the .gro file with a text editor, adjust the number of atoms in 
the .gro file (second line), adjust the topology accordingly, and probably 
re-equilibrate for at least a short period of time.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
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

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