I wasn't sure if I should post this to the gmx-users or gmx-developers list.<br><br>I am constructing coarse-grained CA models for proteins. Adjacent CA atoms are connected by harmonic bonds and sets of three CA atoms are connected by harmonic angles. I have noticed that when a bond angle gets linear (pi) , there is a large spike in the potential energy and that part of the system goes a bit wild (unrealistic high accelerations). I suspect this has to do with the dihedral term, but I'm not sure. In Amber, there was a comment about a disconinuity when a dihedral has a linear angle (I can't find it at the moment). Was this considered when writing gromacs? In all-atom simulations, this is not be a problem, but in these coarse grained methods linear angles are ok, since they are not "real" covalent bonds. Any thoughts/fixes would be appreciated.<br>
<br>Thanks<br><br>-Paul<br>