On 2/28/14, 6:36 AM, abhijit Kayal wrote:
Thanks Justin for the help. But if I want to look the dipole auto
correlation or hydrogen bond dynamics ... is that possible?
Each frame is just a time point in the trajectory. Concatenate the individual
output and you get a time series.
-Justin
On Fri, Feb 28, 2014 at 4:38 PM, Justin Lemkul <jalem...@vt.edu> wrote:
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
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Justin A. Lemkul, Ph.D.
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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 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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