[MMTK] Langevin dynamics using CalphaForceField

Geoff Rollins geoffrey.rollins at ucsf.edu
Fri Sep 5 07:18:34 UTC 2008


I'm interested in running Langevin dynamics simulations using the  
Calpha force field. My understanding is that this force field takes  
every given configuration to be a potential energy minimum, so that  
the gradients will be zero at every time step. The test simulations  
that I've run seem to confirm this since the Calpha's of my protein  
gradually drift away from each other in all directions.

I am wondering if there is any simple way to change the default  
behavior so that only the initial configuration would be a potential  
energy minimum, i.e. the energy and its gradients would not be zero at  
every step. Or, if no simple way exists, I'm wondering what sorts of  
modifications I would need to make in order to achieve this.

Thanks,
Geoff




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