[gmx-users] Problems with pull simulation output - VMD shows broken up groups

[Natalie Stephenson]

Hi,

I've been having a problem with the pull simulation.  After the simulation is complete, I use trjconv to separate the pull file into seperate .gro's and load this into VMD.  When I view it in VMD as the 'video' continues parts of amino acids within the protein structure seem to jump a long way from the rest of that amino acid leaving a long bond between the two, which seems to remain there for the rest of the 'video'.  Can anyone tell me why this might be happening? And if there is a way of solving this problem?

I tried to have a look through the archive for this problem but I have no idea what to even search.

I would be immensely grateful for any light you could shed on this problem.

Thanks in advance.
Natalie


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110303/9b82f07a/attachment.html>