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.war...@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 <soham9...@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 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.