[gmx-users] Density as a function of time

Justin Lemkul jalemkul at vt.edu
Tue Feb 16 18:24:07 CET 2016

On 2/16/16 12:22 PM, Ashutosh Akshay Shah wrote:
> Hello Gromacs Users,
> I want to find the number of ions in a specific part (say left half) of the
> cell as a function of time.
> gmx density gives me a time average value across the box (cell), and I know
> that I can manually find the density for small time steps(0-1,1-2 ns...)
> and plot the values obtained for the left half of the cell as a function of
> time, but it would be much easier to do the same with a single command.
> Any suggestions?

Use gmx select to find the number of ions that satisfy whatever geometric 
criteria you like.



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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