[gmx-users] DSSP problem

[Anton Feenstra]

MOLTENI at unisi.it wrote:
> Hi all
> 
> I have a problem with the "do_dssp" GROMACS module on one of my MD
> trajectories: it is a 8 ns trajectory of a peptide in water and, when I
> run do_dssp on it, the output displays only the first 4440 ps (and the
> program says "last frame: time 4440"), while when I run g_rms on the
[...]
 >
> * I run do_dssp this way: 
> do_dssp -f trajectoryfile -s ....md1.tpr -o ss.xpm -dt 30

This is likely your problem: the '-dt 30' option calculates the modulo
of the time stamp of the frams. Unfortunately, there are unavoidable
rounding errors, which increase with larger numbers. At some point,
the modulo result will be larger than the tolerance value we use, and
the appropriate time frames will not be selected for analysis...

There are two possible workarounds:
* re-set the times on the frames using trjconv -timestep
   then run do_dssp -dt 30
* first create a 30ps interval trajectory using trjconv -skip
   and use that trajectory with do_dssp


-- 
Groetjes,

Anton
  ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
| |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
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