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. The amber coordinate and topology files are also necessary, but will not be delt with here. These files are approximate.

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 minimisation min.in file

 # Minimisation Parameters
  &cntrl
   imin   = 1,
   ncyc = 1,
   maxcyc = 1,
   igb = 2, saltcon=0.2,
   ntb    = 0,
   cut    = 999.0,
   rgbmax = 25.0,
 /

For the minimisation, imin = 1, and no cutoffs cut = 999.0 should be used. Also igb=2 means that we are using the 2nd GB models is expected to perform well on proteins. saltcon=0.2 sets the surrounding (monovalent) salt concentration to 0.2 [mol/L]. ncyc = 1 perform 1 cycle of minimisation maxcyc = 1 perform 1 a maximum number of minimisation steps.

GMIN AMBER input min_md.in file

 # MD  Paramaters
  &cntrl
   imin   = 0,
   tempi = 0.0, temp0 = 700.0,
   ntt = 3, gamma_ln = 1.0,
   nstlim = 500, dt = 0.001,
   igb = 2, saltcon = 0.2,
   ntb    = 0,
   ntc=2,ntf=2,
   ntpr = 100, ntwx = 100, ntwr=100 
   nrespa=1,
   cut    = 8.22,
   rgbmax=8.22,
   ifswitch=1,
   ntr=1,restraint_wt=30.0,
   restraintmask='@N,C,CA',
 /

For the MD steps, imin=0, no minisations are performed. and no cutoffs cut = 999.0 should be used.

Also igb=2 means that we are using the 2nd GB models is expected to perform well on proteins.

saltcon=0.2 sets the surrounding (monovalent) salt concentration to 0.2 [mol/L].

temp1 = 0 sets the initial tempe temp0 = 700 sets final temperature in Kelvin.

.5ps of MD with a 1.0fs time step is set bynstlim=500, dt=0.001

ntt=3 Langevin dynamics with gamma_ln = 1.0 sets frequency of coupling to heat bath to the collision rate of 1 ps-1

ntpr = 100 Energy output frequency ntwr = 100 Restart file frequency ntwx = 100 Trajectory file frequency

ntb = 0 non-periodic, use cutoff for non-bond

ntc=2, ntf=2, use SHAKE to constrain only H bonds (ntc=2) and omit force evaluations for these bonds (ntf=2).

nrespa=2, take a bigger time stepfor evaluating the slow-varying terms in the force field. In this setting, the time step is equal to nrespa * dt ( 2 * 2 fs = 4 fs.

ntr=1,restraint_wt=30.0, set constraint and strength.

rstraintmask='@N,C,CA', constrain backbone atoms only