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

David van der Spoel spoel at xray.bmc.uu.se
Fri Sep 17 13:03:24 CEST 2004

On Fri, 2004-09-17 at 10:44, Kristofer Modig wrote:
> 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"?
There is a function to remove the PBC (used in many analysis tools)
that makes your protein a single molecule. Isn't that what you need?

> Cheers,
> Kristofer Modig
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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