steered_sample

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;