steered_sample

#----------input-----

coordinates             fibrin.pdb

structure               fibrin.psf

parameters              par_all36_lipid_prot_carb.prm

paratypecharmm          on

bincoordinates          minimized.restart.coor

#----------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

fixedAtomsFile fibrin_mod.pdb

SMDOutputFreq 1

SMDDir 0.96568 -0.02529 -0.25849

#---------Scripting

run 200000;