[gmx-users] g_covar

[Anton Feenstra]

Ruben Martinez Buey wrote:
> Hi all,
> I think I got it!
> I get only the backbone in the Structure file with editconf.
> to joining the two individual trajectories I only used the backbone as
> well.
> And now it works, but why not before if you choose only backbone when it
> ask to you
> wich group do you want for the fit?

Trajectories in Gromacs do not contain any information about atom names
or topology. Therefore, all analysis tools assume a one-to-one match
between atoms in the structure file and the trajectory. If you choose
backbone, the program will take e.g. atoms 5, 12, 18, 27 etc. from the
structure file, and also atoms 5, 12, 18, 27 etc. from the trajectory.

That is what we mean when we say 'trajctory and topology files must match':
all atoms in the trajectory must also be in the topology file, in the
same order and without additional atoms inbewteen. The only exception is
atoms at the end of the system (e.g. water), which may be in the topology/
structure file, but not in the trajectory.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
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