[gmx-users] problem with trjconv

[Tsjerk Wassenaar]

Hi Ozge,

Why do you first want to go to a .pdb trajectory? Gromacs comes with
g_hbond, which can analyze hydrogen bonds for you, as well as giving
you an index file containing the atoms involved in hydrogen bonds,
which you can use to extract those from your trajectory. In addition,
g_hbond also does "normal" contacts, other than hydrogen bonds.

Tsjerk

On 2/28/07, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> OZGE ENGIN wrote:
> > 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.
>
> Mark
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
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