Minimization to relax initial bad contacts, explicit solvent
&cntrl
 imin=1, !Minimization
 maxcyc=5000, !maximum number of cycles
 ntmin=2,
 ntpr=1000, !print
 cut=8, !nonbond cut off
 ntr=1, !positional restraints
 restraintmask='@CA,C,N', !restraints on backbone CA, C, N
 restraint_wt=10.0, !weight for positional restraints
 
 iwrap=1,

 icfe=1, ifsc=1, clambda=0.5, scalpha=0.5, scbeta=12.0,
 timask1='@5926,5927,5928,5929,5930,5931,5932,5933,5934,5935,5936,5937,5938,5939,5940,5941,5942,5943,5944,5945,5946,5947,5948,5949,8460',
 timask2='@8450,8451,8452,8453,8454,8455,8456,8457,8458,8459,8463',
 scmask1='@5926,5927,5928,5929,5930,5931,5932,5933,5934,5935,5936,5937,5938,5939,5940,5941,5942,5943,5944,5945,5946,5947,5948,5949',
 scmask2='@8450,8451,8452,8453,8454,8455,8456,8457,8458,8459',
 crgmask='@8463',
 clambda=0.5
&end
