Go REX simulation in MMTSB_1E0Q

To create GO model for molecules, please go to MMTSB GO MODEL BUILDER, Files include    The topology (.top), parameter (.param), and sequence (.seq),   A PDB file representing the native-state conformation is also provided (.pdb), as well as the list of native contacts used in building the potentials (.Qdetails). If data length mismatch error occurred, replace GenUtil.pm in your mmtsb/perl directory.

As a preliminary study, we use 1E0Q as example.
Files under current directory: ./GO_1E0Q.param GO_1E0Q.Qdetails GO_1E0Q.seq GO_1E0Q.pdb GO_1E0Q.Qlist GO_1E0Q.top

To perform temperature replica exchange using GO model, run:

gorex.pl -n 1000 -par initruns=100,equilruns=100 -dir gorex -temp 8:300:500 -log rex.log -charmmlog charm.log -elog energy.log -mdpar steps=1000,fbeta=10.0,timestep=0.02,dynoutfrq=100 -mdopt trajout 1E0Q

After the simulation is done, run:

trajarchive2dcd.pl -inx 1:800 -ref GO_1E0Q.pdb -dir gorex

*discard first 200 runs

then load the trajectories by running:
vmd -e ~/toolset/loadrex.tcl -args gorex

After some adjustment, the trajectory of each replica should look like movie below.


rmsd_grid.sh gorex