[gmx-users] Minimization of Cyclohexane Trappe United Atom

[doerrstein at posteo.de]

Dear Gromacs-Users,


I am trying to simulate Cyclohexane in the NpT-ensemble with the 
Trappe-UA model. So I needed to create my own
ff-folder, where I converted the Trappe-Parameters to 
Gromacs-Parameters. I tried it for molecules like
hexane, pentane and neopentane and for all of them I get quite 
reasonable results. Unfortunately when I try to
minimize united atom cyclohexane, the C-C-C-angles change from 111 
degrees to 100 degrees, which is quite questionable. When I change
the angles in my force-field-folder from 114 to 144 degress the C-C-C 
angles stay approximately at the starting value. After equilibration and 
production the angles
changes, but most of them do not reach

Most of the Trappe-folder is copied from Wes Barnetts website: 
https://github.com/wesbarnett/trappeua

Here is the link with my data: 
https://www.dropbox.com/sh/6y33co2vf9v9fex/AABfpndhgYsUUBpkAyJrhhKLa?dl=0



Maybe someone could give me some advice why this happens and how to 
avoid this problem. Should I worry about this at all?
After equilibration and production runs the angles changes, but most of 
them are still are quite far away from 111 or 114 degrees.

Many thanks in advance...

Best regards,
Mark