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

Natalie Stephenson Natalie.Stephenson at postgrad.manchester.ac.uk
Thu Mar 3 11:16:57 CET 2011


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.

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