[gmx-users] Query regarding g_rmsf and g_hbond

Erik Marklund erikm at xray.bmc.uu.se
Tue Jun 1 09:39:35 CEST 2010

Erik Marklund skrev:
> rituraj purohit skrev:
>> Dear friends,
>> I have some query regarding g_rmsf and g_hbond
>> 1) Through g_rmsf we can plot rmsf Vs atom number (it is by default)
>> but i want to plot  rmsf Vs time, how i can do that?
>> 2) Through g_hbond we can plot number of H-bonds Vs Time (By default)
>> but i want to plot number of h-bonds Vs residues.
>> Is it possible? I tried all the flag given in manual :( but i din not
>> got desire plots.
>> Regards
>> Rituraj
> I think I implemented this feature in g_hbond at some point, but I 
> never pushed it to the master branch. I'll see what I can dig up from 
> the vaults. Until then you can in principle extract that information 
> from the -hbn and -hbm output.
> As for the rmsf issue, isn't this what you get from g_rms?
I think i found one old version of g_hbond that has this feature. 
However, like all older versions it suffers from a memory bug that 
*could* potentially compromize any results that require the existence 
function of the hydrogen bonds. If you're interested, please contact me 
off-list and I'll send you the code.

I think this feature should go into g_hbond in the head branch, but it 
will not happen before the next stable release.

Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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