Steered Molecular Dynamics Example
This is a sample script for running Steered MD in NAMD
#----------input-----
coordinates fibrin.pdb
structure fibrin.psf
parameters par_all36_lipid_prot_carb.prm
paratypecharmm on
bincoordinates minimized.restart.coor
binvelocities minimized.restart.vel
#----------output------
set output pulled
outputname $output
dcdfile ${output}.dcd
xstFile ${output}.xst
dcdfreq 50
xstFreq 50
binaryoutput yes
binaryrestart yes
outputEnergies 50
restartfreq 1000
#---------Basic dynamics-------
exclude scaled1-4
1-4scaling 1
COMmotion no
dielectric 1.0
#--------Simulation space partitioning----
switching on
switchdist 9
cutoff 10
pairlistdist 11
#--------Multiple time stepping----
firsttimestep 0
timestep 1
stepspercycle 1
nonbondedFreq 1
fullElectFrequency 1
#-------Temperature control----
set temperature 310
#temperature $temperature; # initial temperature
#-------Langevin Dynamics------
langevin off; # do langevin dynamics
langevinDamping 1; # damping coefficient (gamma) of 1/ps
langevinTemp $temperature; # bath temperature
fixedAtoms on
fixedAtomsCol B
fixedAtomsFile fibrin_mod.pdb
SMD on
SMDFile fibrin_mod.pdb
SMDk 3
SMDVel 0.001 # Ang/timestep
SMDOutputFreq 1
SMDDir 0.96568 -0.02529 -0.25849
#---------Scripting
run 200000;