Hello, I ran a simulation and after the mdrun some parts of the structure did not generate in vmd, the whole structure was present throughout all of equlibriation just after the mdrun parts disappeared? Any ideas of what might cause this
Hi, Is there all the atoms in place in the pdb file? VMD is behaving differently sometimes and not showing some chains. For my experience this is because vmd could not recognise the end of one chain, tries to connect to the next one and fails because the bond is too long, omitting all the other atoms. As a simple workaround - try to load a structure with correct chain identifiers (right after pdb2gmx for example). Hope that helps.
Yep all my files are correct and when I render the npt and nvt .gro files there’s no missing peices, part of the structure has been modified manually maybe vmd doesn’t like those manually changed parts