Density Restraints

Density Restraints in NAMD

The following script is used to restrain a collect of atoms (referred to as a "component-group") such that they attain a specified target distribution mean position and width in a membrane or membrane-protein simulation, along the transmembrane direction (1-D distribution). The motivation for the restraints comes from diffraction experiments on membrane systems that can be used to measure individual component-group distributions, from which, mean position and width parameters can be extracted. Ideally, the target distribution parameters should come from experimental data. The scripts use the calcForces procedure in NAMD and are therefore written in TCL.

Script: densRestraint.tcl

Additional Files: dbWatDensRest.inp, writeDensRestInp.tcl

Use: Include the following lines in the NAMD inputfile:

tclForces on

tclForcesScript densRestraint.tcl

Note that the name of the restraint input file must be specified at the top of the densRestraint.tcl file

To write the restraint input file using writeDensRestInp.tcl, edit the header of the scripts as necessary and execute it in VMD:

vmd -dispdev text -e writeDensRestInp.tcl

Notes: The component-groups to which the restraint are applied to are defined in the restraint input file, which can be made either by hand, or using the writeDensRestInp.tcl script and an input .pdb file. During the simulation, information about the restraints (current mean position and width, energy of the restraint, etc) are printed to the NAMD output file, which can then be parsed out of the file for later analysis as each line begins with "Restraint_Info:". A simple grep command at the command line can pull these lines out:

grep Restraint_Info test.out > rest.dat