CG-it

CG-it is a VMD package to simplify creating coarse grained (CG) topologies for molecular dynamics simulations. It currently supports CG force fields that follow the "SDK" parameterization procedure from Shinoda et al, Mol Sim, 33:27-36 (2007)

CG-it was developed by Chris MacDermaid chris.macdermaid@gmail.com and Giacomo Fiorin giacomo.fiorin@gmail.com. Special thanks to Axel Kohlmeyer for advice and writing TopoTools. CG-it is available under the GNU General Public License (see COPYING for details).

Install

1. From the main package directory, issue make install to compile and copy the relevant files to ${HOME}/.vmdplugins/ folder.
2. Add the following to your ${HOME}/.vmdrc file:

set auto_path [linsert $auto_path 0 [file join $env(HOME) .vmdplugins]]

3. Start VMD and issue the command (or add it to ${HOME}/.vmdrc for convenience):

package require cg

Example input

To read the parameters database file (available here):

cg readparam parameters.json

To read the topology database file (available here):

cg readtop topology.json

To convert the current VMD molecule from atomistic to CG:

cg map

To assign the types of bonded interactions (not all commands may be needed):

cg setbonds
cg setangles
cg setdihedrals
cg setimpropers

To add water to the system if not already present (unit cell must be defined):

cg solvate

To finalize the CG topology:

cg reanalyzemol

To get the full help invoke the cg command without arguments:

cg help