# sample NAMD configuration file for INITIAL Dynamics w/ fixed atoms

timestep                2.0
stepspercycle           10

fullElectFrequency      1
nonbondedFreq           1

# molecular system
coordinates		output_building/d1_d2.pdb
structure 		output_building/d1_d2.psf
temperature             300

# restraints

fixedAtoms              on
fixedAtomsForces        on
fixedAtomsFile		output_building/d1_d2_fixed_atoms.pdb
fixedAtomsCol           B

# force field
paratypecharmm          on
parameters              	../common/par_all27_prot_na.inp

# approximations
exclude                 scaled1-4
1-4scaling              1.0
switching               on
switchdist              10
cutoff                  12

# neighbor lists

pairlistdist            12
margin                  2

# shake

rigidBonds              water
rigidTolerance          0.00001  # default
rigidIterations         500      # default

# temperature control

langevin                on
langevinDamping         1
langevinTemp            300
langevinHydrogen        no

# output

outputname              output/min_dyn0
binaryoutput            no

DCDfile                 output/min_dyn0.dcd
DCDfreq                 1000
DCDUnitCell             yes
wrapAll                 on

# restart files

binaryrestart           no
restartsave             no
restartname             output/min_dyn0.rest.pdb
restartfreq             10000

# screen output

outputenergies          20
outputtiming            100

# run control
minimize                10000
run	                10000



