NAMD supports the SMOG model from published from Onuchic's lab [77,78]. The input files for SMOG can be generated from the SMOG website (http://smog-server.org) . It is recommended to run these simulations with 1-4 exclusions (as opposed to scaled 1-4), a 0.5fs timestep, and with a 0.5fs timestep (as described in [77,78]).
As the SMOG model uses GROMACS topology and coordinate files, the GROMACS configuration parameters--gromacs, grotopfile, >rocoorfile--must be defined. The description for the GROMACS configuration parameters are reproduced below:
To run a SMOG simulation, the following extra parameters must be defined.