[gmx-users] Combined essential dynamics

[Anton Feenstra]

Sekar Ramachandran wrote:
> Hi,
> I am trying to carry out a COMB_ED analysis of two
> forms of the  protein. I have carried out 5ns
> simulations of the two proeins. I want to use 1 ns to
> 5ns data from the two trajctories to run an essential
> dynamics analysis. I created a tpr file for both
> protiens containing only the CA atoms. I concatenated
> the two trajectories using the folloing command:
[...]
> is 0.0 angstroms). This makes me believe that there is
> something wrong with the way I ahve carried out my
> analysis. I would be really grateful to anyone who cna
> help me with this.

It seems to me you used a .tpr (topology) file with only CA atoms, while
your trajectories (.trr) contain the whole protein. That doesn't work.
Your .tpr and trajectory *must* match atom-for-atom. If you want to analyse
a subset, that is easily done by selecting a group (default group or from
an .ndx file) in g_covar & g_anaeig (must be same group).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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