Estimation of the free energy of the Arg381-Asp410 salt bridge

For the umbrella sampling part, the overall workflow follows the PLUMED tutorial detailed in 

https://www.plumed.org/doc-v2.8/user-doc/html/belfast-4.html,

Specifically, the plumed files for each window are prepared as 
"

for AT in 0.38 0.40 0.42 0.44 0.46 0.48 0.50 0.52 0.54 0.56 0.58 0.60 0.62 0.64 0.66 0.68 0.70 0.72 0.74 0.76
 do

cat >plumed.dat << EOF
dDR: DISTANCE ATOMS=6098,6580
restraint-dDR: RESTRAINT ARG=dDR KAPPA=60000.0 AT=$AT
PRINT STRIDE=10 ARG=dDR,restraint-dDR.bias FILE=COLVAR$AT
EOF

gmx_mpi mdrun -plumed plumed.dat -nsteps 25000000 -x traj$AT.xtc

done
"

For the steered MD part, the overall workflow also follows the PLUMED tutorial detailed in 

https://www.plumed.org/doc-v2.8/user-doc/html/belfast-5.html,

where the plumed script is prepared as

"

dDR: DISTANCE ATOMS=6098,6580
MOVINGRESTRAINT ...
  ARG=dDR
  STEP0=0 AT0=0.38 KAPPA0=50000.0
  STEP1=10000 AT1=0.62
...

PRINT STRIDE=10 ARG=* FILE=COLVAR
"

The methods and scripts for post-analysis are identical as these tutorials.