Hello. I have some issues with representing “gro” file in VMD. First of all, I am studying coarse grained polypropylene and I am using Martini Force Field in Gromacs 5.0.7. Specifically, when I am loading the “gro” file, in Graphics/Representations field I can use “Lines” and “Dynamic Bonds”, but if I choose “VDW” it seems like interpretering my system as individual atoms. I am attaching the “gro” file. Any idea why is this happening?
Thank you in advance.
Because VMD guesses bonds from distances, which are often very long in CG models. Most VMD features assume atomistic models.
If you have questions about VMD, you should ask them via the VMD mailing list.
Thanks a lot. Is there any way to fix this problem? I will ask also via VMD mailing list.
VMD needs topological information (bonded connectivity) from formats like PSF, etc. Unfortunately, I do not think VMD reads any GROMACS-formatted topology.