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.
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