[gmx-users] traj comparison

[Anton Feenstra]

giacomo de mori wrote:
> 
> Dear Gromacs users,
> we would like to compare two trajectories of two peptides with the same
> sequence, one containing an SS bond and the other without it (different
> topology files). We would like to compare them to a common backbone
> structure and obtain matrix in .xpm format of comparison values of each
> structure in the 1st trajectory with respect tothe other (like -f2
> option in g_rms). Is there an easy way to overcome the different
> topology problem?

Yes, although it may seem a bit awkward. If you only want to compare
the backbone, use trjconv to generate backbone-only trajectories for
both peptides and use tpbconv to generate backbone-only topology files
(by the way, for g_rms a backbone-only .gro file will also do).
Then use the set of backbone-only files in g_rms...

-- 
Groetjes,

Anton
 ________ __________________________________________________________
|        | Anton Feenstra                                           |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam   |
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| ' __   | Feenstra at chem.vu.nl - www.chem.vu.nl/afdelingen/FAR      |
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