[gmx-users] constraining secondary structure gmx 5

Yoav Atsmon-Raz yoav.atsmonraz at ucalgary.ca
Thu Dec 10 17:17:33 CET 2015

I've been trying to run a gromacs simulation of alternating d/l cyclical peptides (yes I know this is a dead horse that's been beat one time to many...) and after a lot of experimentation I managed to get an initial setup working via charmm gui. However, as the simulation progresses the structure becomes completely unstable which doesn't fit the experimental results that I'm familiar with in the literature. I was wondering if there is any way to manually constrain a secondary structure on a per residue basis beyond the definitions in the posre file. The reason I'm asking this is that I'm aware that this is possible in CHARMM and NAMD but I can't seem to find anything detailing this in the gromacs manual.

Thanks to anyone responding to this!

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