Hi lammps users,
We've run into a problem using the Dec 3rd. 2010 version of lammps, a dcd output and a triclinic cell: Visualizing the dcd file using vmd results in a strange cell size/orientation. What we think is wrong is the order of the cell parameters being written with each step. In lines 136-156 in dump_dcd.cpp in lammps, the cell size/orientation is written in order:
a, alpha, b, beta, gamma, c
where a, b, c are lengths and alpha, beta, gamma are the cosine of angles.
However, according to the dcd plugin in vmd, the cell parameters are read in order:
a, gamma, b, beta, alpha, c
See lines 1090-1095 on this site: http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/dcdplugin_8c-source.html. I couldn't tell you if this is an issue with lammps or vmd since I can't seem to find a spec somewhere that I can make heads or tails of, does anyone know?
Cheers,
Andrew
Hi lammps users,
We've run into a problem using the Dec 3rd. 2010 version of lammps, a dcd output and a triclinic cell: Visualizing the dcd file using vmd results in a strange cell size/orientation. What we think is wrong is the order of the cell parameters being written with each step. In lines 136-156 in dump_dcd.cpp in lammps, the cell size/orientation is written in order:
a, alpha, b, beta, gamma, c
where a, b, c are lengths and alpha, beta, gamma are the cosine of angles.
However, according to the dcd plugin in vmd, the cell parameters are read in order:
a, gamma, b, beta, alpha, c
See lines 1090-1095 on this site: http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/dcdplugin_8c-source.html. I couldn't tell you if this is an issue with lammps or vmd since I can't seem to find a spec somewhere that I can make heads or tails of, does anyone know?
andrew,
it has to be a bug in lammps, since i used the vmd molfile plugin
as reference for implementing triclinic cell support into the dcd plugin.
i'll have a look at it later today and send a patch to steve.
axel.