I have a functional simulation of 7 polymer chains, and when I use VMD to visualise my output, the chains are all mixed up -- it is still a polymer, but now atoms from one chain are randomly incorporated into other chains ( if I colour my chains any one chain has all the possible colours in it). However, when I visualise the same output in gnuplot, I get separate polymer chains. I suspect that my problem might be related to bond guessing in VMD? Is there anything I could do about this?
Thank you very much in advance!
With best wishes,