Dear all, I wish to know what is the best way to visualize gromacs trajectory.
When I load a gromacs trajectory into VMD, I find some of the water molecules and some part of the protein in the system are streched and the structure become weild and cannot be properly analyzed. I searched google and found there is a gromacs plugin for vmd, but I don't know whether it will help improve gromcas trajectory visualization ( https://www.ks.uiuc.edu/Research/vmd/plugins/updates/vmd192_gromacs_update1/ ). I also found there is a gromcas plugin for pymol ( https://bioexcel.eu/run-gromacs-within-pymol-with-dynamics/). But it seems to be used for simulation. It doesn't seem to be used to load and visualize a extraneous the gromacs trajectory. What are your suggestion？ Thank you in advance. Yeping -- 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.
