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

2013-02-19 Thread Erik Marklund
On Feb 19, 2013, at 10:19 AM, Kavyashree M wrote: Dear users, *When I use g_hbond with -contact and -r 0.4 on C-alpha atoms -* I get the following message - *** Reading frame 0 time 4000.000 Will do grid-seach on 26x

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

2013-02-19 Thread Erik Marklund
Try a more recent versions. There were a bunch of bugfixes since 4.5.3 Erik On Feb 19, 2013, at 10:19 AM, Kavyashree M wrote: Dear users, *When I use g_hbond with -contact and -r 0.4 on C-alpha atoms -* I get the following message -

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

2013-02-19 Thread Kavyashree M
Dear users, *When I use g_hbond with -contact and -r 0.4 on C-alpha atoms -* I get the following message - *** Reading frame 0 time 4000.000 Will do grid-seach on 26x26x19 grid, rcut=0.4 Last frame500 time 5000.0

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

2013-02-18 Thread Kavyashree M
Sir, My purpose was to compare two simulations of the same protein at different temperatures. So I wanted to see how the interaction of each residue with other residues, within a cut-off, varies between the two. by using the matrix of C-alpha contact over the whole trajectory. Thank you kavya On

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

2013-02-18 Thread Kavyashree M
Hello Sir, I used C-alpha atoms. Kavya On Mon, Feb 18, 2013 at 11:28 PM, Erik Marklund wrote: > 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

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 use

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

2013-02-18 Thread Kavyashree M
Dear users, As Suggested by Erik, I used g_hbond with -contact to obtain a matrix of each contact as a function of time. I used the following command - g_hbond -f a.xtc -s a.tpr -contact -r2 0.5 -hbm m.xpm -b 4000 -e 4400 -hbn c.ndx I get only three contacts in the index file. The protein is a d

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 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 function of

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 give

[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 http://lists.