Running GMIN with MD move steps AMBER

Running GMIN with AMBER with MD move steps can be more efficient than with random cartesian move steps. To do so one needs the GMIN input file data, the AMBER file min.in for defining the energy function used whilst minimising, and the AMBER file min_md.inf or defining the energy function, parametrs for the MD move steps.

GMIN input data file

 SLOPPYCONV  1.0D-2              
 TIGHTCONV   1.0D-3              
 UPDATES     8000                
 MAXERISE 0.001                  
 STEPS 100  1.0                  
 STEP  0.00 0.0      
 AMBER9 coords.inpcrd inpcrd          
 AMBERMDSTEPS                    
 MAXIT 10000 10000               
 MAXBFGS   1.0                   
 TEMPERATURE  1.0                
 RADIUS 300.0                    
 DUMPSTRUCTURES                 

GMIN AMBER minimization min.in file

 # Minimization Parameters
  &cntrl
   imin   = 1,
   ncyc = 1,
   maxcyc = 1,
   igb = 2, saltcon=0.1,
   ntb    = 0,
   cut    = 999.0,
   rgbmax = 25.0,
 /

GMIN AMBER input min_md.in file

 # MD  Paramaters
  &cntrl
   imin   = 0,
   tempi = 700.0, temp0 = 700.0,
   ntt = 3, gamma_ln = 1.0,
   nstlim = 500, dt = 0.001,
   igb = 2, saltcon = 0.1,
   ntb    = 0,
   ntpr = 350, ntwx = 10,nrespa=1,
   cut    = 999.0,
   rgbmax=8.22,
 /