[gmx-users] (no subject)

Justin Lemkul jalemkul at vt.edu
Fri Feb 28 12:10:19 CET 2014

On 2/28/14, 5:38 AM, abhijit Kayal wrote:
> Dear Gromacs users,
>         My system contained CNT+ water. I have created a dynamically
> index.ndx file
> which contain the number of water molecules in each frame inside cnt.
> Now I want to study the dipole orientation of these water molecules. But I
> can't select all the groups at a time. From the mailing lists search I came
> to know that any gromacs analysis tools can't do this. So is there any
> other way to do these type of analysis. I am using gromacs 4.5.5.

You have to analyze each frame individually rather than processing the 
trajectory in one pass.  With a simple shell script, you can loop through the 
index groups, write out a corresponding frame from the trajectory, then analyze it.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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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