Dear GROMACS Users, I am trying to visualize the simple polyethylene chains (multiple chains) consisting of certain number of atoms generated using RIS theory using VMD. I'm using the PDB format to express coordinates to visualize my chains. The chains are very random and at some points multiple atoms of a chain comes very near to each other. Sometimes, even there is inter chain overlapping and multiple atoms of different chains comes in close vicinity of each other. In such a situation, while visualizing via. VMD, there appears a bond between those close or very close atoms within a chain or between two chains. Therefore, the visulaization by VMD shows that number of bonds is much greater than the number of atoms and forms a cage like structure (in some cases) between the closely spaced or overlapping atoms. What might be the possible cause of this ? Does VMD connects Atoms taking in some distance criterion ? Can we change that distance criteria that VMD utilize to connect the atoms of a polymer chain in succession ?
Thanks and Regards-- Abhishek -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
