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

[Dallas Warren]

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.

http://manual.gromacs.org/documentation/current/onlinehelp/gmx-velacc.html#options
http://manual.gromacs.org/documentation/current/onlinehelp/gmx-h2order.html#options
http://manual.gromacs.org/documentation/current/onlinehelp/gmx-hydorder.html#options

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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