[gmx-users] do_dssp problem

Erik Marklund erik.marklund at chem.ox.ac.uk
Tue Mar 22 19:54:39 CET 2016

Dear Khatnaa,

I would certainly downsample using -dt. Unless, of course, you really need to know the secondary structure over 300000 frames. That said, I think do_dssp should be able to handle large trajectories, so this might be a bug in some sense.

Kind regards,

> On 22 Mar 2016, at 16:07, badamkhatan togoldor <bdmkhtn at yahoo.com> wrote:
> Dear Gmx-Users,
> I had done roughly 300ns peptide and membrane simulation. I am trying to do some analyses through the do_dssp. To get in .xpm file I put .xtc and .tpr files. Then at certain frame its just killed and gave me the empty files with strange names like ddccTf1j, ddmMD9pt, ddmuWFKI....in this case what should i do? reduce the reading frame number (300.000 frames)? or is it cluster related issue? Any advices and helps will be highly appreciated !         
> Regads, 
> Khatnaa
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