Running SMOG simulations

SMOG model considerations

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) [54]. 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]).

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:

• gromacs $<$ use GROMACS format force field? $>$
  Acceptable Values: on or off
  Default Value: off
  Description: If gromacs is set to on, then grotopfile must be defined, and structure and parameters should not be defined.
• grotopfile $<$ GROMACS format topology/parameter file $>$
  Acceptable Values: UNIX filename
  Description: This file contains complete topology and parameter information of the system.

• grocoorfile $<$ GROMACS format coordinate file $>$
  Acceptable Values: UNIX filename
  Description: This file contains the coordinates of all the atoms. Note that coordinates can also be used for PDB format coordinate file. When gromacs is set to on, either grocoorfile or coordinates must be defined, but not both.

To run a SMOG simulation, the following extra parameters must be defined.

• GromacsPair $<$ Are GROMACS pair forces turned on? $>$
  Acceptable Values: on or off
  Default Value: off
  Description: This variable determines if the pair section of the GROMACS topology file grotopfile is evaluated. Currently, only Lennard-Jones type pairs are supported. Variable is only used if gromacs variable is `on'.

• staticAtomAssignment $<$ Optimization to fix atoms onto a specific node $>$
  Acceptable Values: on or off
  Default Value: off
  Description: Specifies if atoms should be statically fixed to a node. This will change the internode communication and will give a significant speed-up to MD simulations if the atoms are moving rapidly. It is suggested that SMOG simulations use the staticAtomAssignment flag.