[gmx-users] Query regarding g_rmsf and g_hbond

[Erik Marklund]

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/