[gmx-users] RE: gmx-users Digest, Vol 105, Issue 5

[Julio Dominguez]

First of all Happy New Year to everyone. Second, Justin I admire you. You keep this forum alive and very well tended. Great job.Third, Parisa, try running do_dssp with the flag -dt and pick an interval one or two orders of magnitude smaller than the length of your simulation. That should do it.
Best regards.

> Message: 7
> Date: Tue, 1 Jan 2013 22:47:39 +0330
> From: Parisa Rahmani <rahmani.prs2 at gmail.com>
> Subject: Re: [gmx-users] secondary structure analyze
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
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> 	<CAAC4-TsTT+PGWo04AVj64HFLvkZ8mnsQRF-uUgykBUXCS5RdPg at mail.gmail.com>
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> 
> Thanks Justin for the reply,
> how i can sure that it uses the DSSP package correctly ,
> it seems that it just uses the gromacs code :
> (
> Opening library file /home/parisa/parisa/share/gromacs/top/phbres.dat
> Opening library file /home/parisa/parisa/share/gromacs/top/aminoacids.dat
> Opening library file /home/parisa/parisa/share/**gromacs/top/ss.map
> )
> for some reasons I use gromacs 3.3.3.