Hi Sangeeta,
It would be helpful to us if you gave more information than "I tried
to run a simulation and it crashed". What kind of protein, any
ligands/non-standard groups. Did you perform energy minimization, etc,
etc, etc... What's in the .mdp file?
Tsjerk
On 3/15/07, Erik Marklund <[EMAIL PROTECTED]> wrote:
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
[EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
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