On Mar 7, 2013, at 11:45 PM, Michael Kuiper wrote:
Greetings Samuel!
Please feel free to use any movies I send you any way you like. I hope to have some more later.
I think I've found a bug in 2.11 with regards to writing out large pdb files. (I'm not quite sure the official way to report this)
I'm not sure i like how the fora work .. so for now writing to rnatoolbox-help@simtk.org is best
It seems to me that if there are more than 100000 atoms, we will see a shift in the x,y,z coordinates due to the limitations in the pdb format in the atom number column. I've written a small python script that corrects these errors for myself but it is easier to do it in the source!
If your molecules are big you should just see a reduction in the precision. Can you send me your commands.dat and input structure file?
The error means that the large molecule trajectories are not displayed properly in vmd and also restarting from a 'last.x.pdb' file also seems corrupted.
For large atom numbers I use hexadecimal notation in pdb files.
Have to run to a meeting, chat soon!
Mike