[gmx-users] pbc-replica exchange-trjconv

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Jun 11 16:48:29 CEST 2008

Hi Servaas,

> trjconv -f fit.trr -o cluster.trr -n lig_prot.ndx -pbc cluster -s top140.tpr

I think there's quite a bit of reason to start calling you names here :)
Assumedly, fit.trr means that it results from fitting the trajectory
to a reference?
So what does this do with your PBC?

> I also tried the -nojump option and after this the whole option but in
> visualistion (with VMD) I got strange bonds...

Right, so strange bonds should be quite an indication that there's
something weird with your shifts.

> An often reported problem was that the the structure in the tpr file is not
> close enough to the starting structure in the trajectory, I tried it by
> making a tpr file with a the strating structure of the trajectory (in this
> structure the ligand is in the active site if I look at the structure). But
> this did not help.

Another often, or at least several times, mentioned problem relates to
the fact that fitting a structure reorients the molecule, but leaves
the PBC as it is, causing a mismatch between the system and the PBC.
Therefore one can not execute any PBC related operations (nojump,
cluster, whole), after the trajectory has been fitted.

No hard feelings ;)



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
F: +31-30-2537623

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