[gmx-users] trjconv -pbc cluster

[David van der Spoel]

On Wed, 2004-09-01 at 13:50, Anton Feenstra wrote:
> Hi,
> 
> 
> I'm trying to keep two peptide monomers together for, e.g., rmsd analysis.
> However, trjconv -pbc cluster gives me:
> 
> Select group for clustering
> Selected 1: 'Protein'
> Select group for output
> Selected 1: 'Protein'
> Back Off! I just backed up cluster2.xtc to ./#cluster2.xtc.1#
> 20470.000    ->  frame    470 time 20470.000
> COM:    0.889     0.440     4.394  iter = 1
> COM:    4.016     3.566     4.394  iter = 2
> COM:    0.889     0.440     4.394  iter = 3
> COM:    4.016     3.566     4.394  iter = 4
> 
> ad infinitum... I've tried continuing from a later frame, e.g. '-b 20500'
> but that doesn't help, it gives this error right away at frame t=20500.
> 
> Any hints, anyone?
Very unlikely that this would happen. You might be able do it in two
rounds, first you center the first peptide in the central box, then you
do the clustering.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone:  +46 18 471 4205  fax: +46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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