[gmx-users] User-written analysis programs and protein jumping

Kristofer Modig kmo at apk.molbio.ku.dk
Fri Sep 17 10:44:39 CEST 2004

Dear someone,

I read somewhere in the archives that the standard analysis programs
take care of the protein "jumping" within the periodic boundary, so that
converting with "trjconv -center -pbc nojump" should not be necessary. I
wonder if the same apply if I write my own analysis program according to
the supplied c template? My goal is to do a non-standard analysis of the
N-H bond dynamics, so I want to be sure that the jumping does not affect
this in any strange way. In other words, does the
read_next_frame() function return atom coordinates that are corrected
for the "jumping"?

Kristofer Modig

Kristofer Modig, Ph. D.
mail:  kmo at apk.molbio.ku.dk
www:   http://dupont.molbio.ku.dk
phone: +45 353 22079

Department of Protein Chemistry
Institute of Molecular Biology
University of Copenhagen
Øster Farimagsgade 2A, 4.
1353 Copenhagen K

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