cat <<eof > mdin
  run MD at 300K 
 &cntrl
   ntc=2, ntf=2,
   cut=12.0, igb=2, saltcon=0.2, gbsa=1,
   ntpr=50, ntwx=50,
   nstlim = 500, dt=0.002,
   ntt=1, tempi=300.0, temp0=300.0, tautp=2.0,
   ntx=1, irest=0, ntb=0,
   nscm = 1000,
 &end
eof
sander   -O -i mdin \
-c trx.equil.rst  -p trx.top  -o trx.md.out -x trx.md.x -r trx.md.rst