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Subsections


Running SMOG simulations

SMOG model considerations

NAMD supports the SMOG model from published from Onuchic's lab [118,119]. The input files for SMOG can be generated from the SMOG website (http://smog-server.org) [82]. 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 [118,119]).

Configuration file modifications

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.


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Next: Constant-pH Simulations 1 Up: Structure based simulations Previous: Hybrid MD-Go Simulation   Contents   Index
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