[gmx-users] trjconv - whole/nojump

Rainer Boeckmann rboeckm at gwdg.de
Mon Aug 5 11:33:14 CEST 2002


concerning the "problem" of ending with whole molecules without jumps due to
periodic boundaries one 'has' to take the whole continuous trajectory, a run
input file with whole molecules, then run first trjconv -pbc whole and after
that  trjconv -pbc nojump (and not the other way around as stated somewhere

An alternative for PARTS of very long trajectories would be to construct run
input files for example every 5th nanosecond (for lipids this will be
sufficient) or so. Otherwise the nojump-option will break the molecules again.

Thanks to Peter  and David!

Rainer Böckmann
Theoretical Molecular Biophysics Group
Max-Planck-Institute for Biophysical Chemistry
Am Faßberg 11
D-37077 Göttingen

Tel.: +49(551)201-1141, Fax.: +49(551)201-1089
email: rboeckm at gwdg.de


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