[gmx-users] problem with trjconv

Mark Abraham Mark.Abraham at anu.edu.au
Wed Feb 28 15:47:30 CET 2007

> Hi,
> I have a problem with the trjconv command. 
> I performed a 30 ns simulation, and wanted to analyze hydrogen bonds formed between protein and water molecules. In this respect, I converted the xtc file into a pdb file by selecting system option. As you can understand the overall file was such a large file that I could not handle it. So, I want to know whether there is any possibility to select water molecules within a cutoff value or to extract frames within  given time steps? For instance, at every 70 th step, from 70 ps to 80 ps.

If you read the man page for trjconv, you will see an option to do the 
latter. I don't think the former is implemented in the gromacs utilities.


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