Constant Velocity Pulling

We will try to stretch the APOMYOGLOBIN through constant velocity pulling method. In this simulation we attach a dummy atom to SMD atom via virtual spring, and the dummy atom is moved with a constant velocity.
Change the directory to cvp.
We use vmd to prepare files for simulation. Load the psf and pdb files to vmd. In the Extensions $>$tkcon, type

set allatoms [atomselect top all]
$allatoms set beta 0
set fixedatom [atomselect top "resid 1 and name N"]
$fixedatom set beta 1
$allatoms set occupancy 0
set smdatom [atomselect top "resid 153 and name CA"]
$smdatom set occupancy 1
$allatoms writepdb newmyo.ref
set smdpos [lindex [$smdatom get {x y z}] 0] 	 
set fixedpos [lindex [$fixedatom get {x y z}] 0] 	 
vecnorm [vecsub $smdpos $fixedpos]

Output is three numbers, which are x, y, and z components of end to end unit vector. These will be used in the NAMD configuration file. The relevant part of configuration file(myo_cve.namd) is given below.

#fix one atom
fixedAtoms on
fixedAtomsFile newmyo.ref
fixedAtomsCol B

#SMD
SMD      on
SMDFile  newmyo.ref
SMDk     5.0         ; # approx 350pN/A
SMDVel   0.001       ; # 1 A /ps
SMDDir  -0.561 -0.566 -0.605  ; # dirn of endtoend vec
SMDOutputFreq  500     ; # every 1 ps

Issue the command

mpirun -np 16 /usr/local/namd/namd2mpi/ myo_cvp.namd > cvp.log &

to run the simulation. Quick analysis of the log file is done using smdanaly

 ./smdanaly cvp.log

.