Re: [gmx-users] Use of index file generated by gmx select
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 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 25 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.
[gmx-users] Use of index file generated by gmx select
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 25 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.
[gmx-users] Use of index file generated by gmx select
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 25 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.
[gmx-users] Use of index file generated by gmx select
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 25 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.
