Re: [gmx-users] Number of interactions per residue

2013-02-18 Thread Erik Marklund
Hi, With -r2 one can provide a second, larger, cutoff so that contact kinetics can be analyzed within the Luzar-Chandler framework that were designed for hbonds. What index groups did you use? Erik On Feb 18, 2013, at 6:04 PM, Kavyashree M wrote: Dear users, As Suggested by Erik, I

[gmx-users] Number of interactions per residue

2013-02-14 Thread Kavyashree M
Dear users, How can I get the number of interactions of each residue within a cut off as a function of time. just like g_saltbr writes with the option -sep. I tried using g_mdmat but it gives an average contact map. Thank you Kavya -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Number of interactions per residue

2013-02-14 Thread Erik Marklund
Perhaps g_hbond -contact will do what you want. Erik On Feb 14, 2013, at 10:42 AM, Kavyashree M wrote: Dear users, How can I get the number of interactions of each residue within a cut off as a function of time. just like g_saltbr writes with the option -sep. I tried using g_mdmat but it

Re: [gmx-users] Number of interactions per residue

2013-02-14 Thread Kavyashree M
Thank you! On Thu, Feb 14, 2013 at 3:38 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Perhaps g_hbond -contact will do what you want. Erik On Feb 14, 2013, at 10:42 AM, Kavyashree M wrote: Dear users, How can I get the number of interactions of each residue within a cut off as a