[gmx-users] DSSP hangs for days

Mark Abraham Mark.Abraham at anu.edu.au
Sun Jun 28 16:40:11 CEST 2009

sharada wrote:
> Hi,
>  I waited for it to finish for  almost 5 days nothing happened 
> except creation of  those files.  I had posted a similar  mail some time 
> back. Is there no solution for this.  Is it something to do with speed 
> of the system?  I ran the program on HP dual core system.

The length will scale linearly with the number of frames in your 
trajectory. New users frequently do this analysis on every one of a 
million snapshots, which is a waste of effort. First, do it on a 
trajectory with a few snapshots to test. If that takes longer than a few 
minutes, you haven't installed DSSP or told GROMACS where to find it. 
Read the DSSP documentation and do_dssp -h.


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