[gmx-users] Use of index file generated by gmx select

Dallas Warren dallas.warren at monash.edu
Sun May 26 23:36:48 CEST 2019

gmx scripts have the -n switch, which you can use to pass an index.ndx
file to, then control which particles the script then applies the
analysis too.


Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Sat, 25 May 2019 at 19:42, Soham Sarkar <soham9038 at gmail.com> wrote:
> Hello,
>     I have a 500ns trajectory of protein-water-urea mixture, saved at 2ps
> interval. I am using gmx select to generate a index.ndx of 250000 index for
> water molecules within 0.5nm of the protein. I want to know how to use this
> index.ndx file for my calculation -
> For example:
> a) If I want to calculate the velocity autocorrelation using gmx velacc of
> those water molecules within 0.5nm of the protein.
> b) The orientation of those  water molecules using the dipole of water
> using gmx h2order
> c) The tetrahedral order parameter for those particular water molecules
> how should I use the index file? Please provide me with the command and the
> process of calculation.
> Thanks and regards-
> Soham
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