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
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