[gmx-users] how long it take to run do_dssp

Xavier Periole X.Periole at rug.nl
Mon Oct 6 18:06:37 CEST 2008

On Mon, 6 Oct 2008 17:27:31 +0200 (CEST)
  "Morteza Khabiri" <khabiri at greentech.cz> wrote:
> Dear gmxuser
> I want to analyze the secondary structure of a protein after a
> 10ns simulation run but I do not know how long it will take because I run
> it for more than 2 hours but it is still running.I don't know whether I am
> encountering any problem , in  the manual it is mentioned that the program
> is very slow. But it is not mention how long.
> I saw in gmx mailing list that somebody has my problem before but his
> problem solved by my_dssp.
> Unfortunately, I could not also run my_dssp and I faced with many error.
Do it first on one conformation, then 10 from the trajectory (-b -e options)
and you can get an estimate.
> tnx
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XAvier Periole - PhD

- Molecular Dynamics Group -
NMR and Computation
University of Groningen
The Netherlands

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