[gmx-users] problem regarding "mdrun" and "g_hbond"

[Erik Marklund]

15 mar 2007 kl. 08.29 skrev sangeeta kundu:

> Dear all,
>       I gave a simulation run of a protein using G43a1force field  
> at 523K using Berendson's  Temperature  coupling for 10 ns, But  
> three times it failed with the messege "segmentation fault" ,  
> without giving any other error messege. Previously I ran the  
> simualtion of the same protein at lower temperature, (upto 473K) ,  
> and in all cases it ran successfully, but when I used the  
> temperature of 523 K it failed, I can not debug, please help.
>

I'm no expert, but I think a shorter timestep could be required for  
the integrator to be stable when using such high temperatures, since  
the atoms will move around quite fast.

>      I have another question, Is there any way of analysing  
> hydrogen bonds on a residue basis? I mean to say how can  I get the  
> distribution of HBond over residue number, I  looked at g_hbond ,  
> but I could not get it.
>

It requires some postprocessing of the data, but the hbn- and hbm- 
output of g_hbond together contains what you need to know about the  
hydrogen bonds on an atom index basis. Now, you can easily go from  
the level of atoms to the level of residues.

>
> regards
> Sangeeta
>
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_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
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://xray.bmc.uu.se/molbiophys


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