Using GMIN to generate endpoints

We can use GMIN to explore the energy landscape of our peptide and find interesting structures (endpoints) to connect using OPTIM and PATHSAMPLE. Copy the coords.prmtop and coords.inpcrd files you just made into a new directory, and add the following file:

data - the GMIN input file

COMMENT DEBUG
SLOPPYCONV 1.0D-5
TIGHTCONV 1.0D-6
MAXERISE 1.0D-4
DUMPINT 100
UPDATES 1000
MAXIT 20000 60000
MAXBFGS 1.0
TRACKDATA
DUMPSTRUCTURES
TEMPERATURE 1.0
SAVE 20
STEPS 100 1.0
STEP 0.0
RADIUS 300
AMBERMDSTEPS
AMBER9 coords.inpcrd inpcrd

See the GMIN documentation for the explanation of these keywords!

min.in - the AMBER (SANDER) settings for minimisation

STOP
 &cntrl
  imin   = 1,
  ncyc = 1,
  maxcyc = 1,
  igb = 2, saltcon=0.1,
  ntb    = 0,
  cut    = 999.99,
  rgbmax = 25.0,
  ifswitch = 1
 /

The line "igb .." species the Generalized Born implicit solvent model used. For vacuum, use igb=0 and delete "saltcon" keyword.

min_md.in - the AMBER (SANDER) settings for molecular dynamics (used to generate new conformations for basin-hopping)

STOP
 &cntrl
  imin   = 0,
  tempi = 600.0, temp0 = 800.0,
  ntt = 3, gamma_ln = 3.0,
  nstlim = 1000, dt = 0.001,
  igb = 2, saltcon = 0.1,
  ntb    = 0,
  ntpr = 1000, ntwx = 0,nrespa=1,
  cut    = 999.99,
  rgbmax = 25.0,
  ifswitch = 1,
/

You can run GMIN now to generate some low energy structures:

AMBGMIN &