[gmx-users] Analyzing With Indices Created By GMX Select

[Justin Lemkul]

On 7/6/16 2:41 PM, ALEXANDER DHALIWAL wrote:
> Hi All,
>
> I am having a problem. Using GMX Select, I have selected for some molecules
> within my simulation; namely, a solute of interest and the phospholipids
> surrounding it within a radius of 2 nm. This was done using the following
> command:
>
> gmx select -f md_2_25_cat.trr -s md_2_25_cat.tpr -n all_groups.ndx -on
> select.ndx
> ...
> group 5
> group 7 and within 2 of resid 138
> ctrl+D
>
> This generates an index file with an independent group for every frame of
> my simulation, as the molecules contained within this designation change as
> time goes on. However, I am now unsure about how to use this index file in
> any analyses. For instance, if I want to calculate the hydrogen bonds
> between this group and the surrounding solvent, is there a way to assign a
> new pairs of groups for every frame of the simulation (i.e., group SOL +
> group Fr1 for Frame 1; group SOL + group Fr2 for Frame 2, etc)? Currently,
> I can only compare it to a single frame group, and this isn't very helpful.
> If anyone can help me with this, it would be much appreciated!
>

Dynamic indices are not smoothly integrated into most analysis programs yet, so 
frame-by-frame is the only way to go in most instances.  Easily done with a loop 
in a shell script.

-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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