Evaluating different components of AMBER energy function with SANDER

Editing Evaluating different components of AMBER energy function with SANDER

After running AMBGMIN, it is informative to examine the different components of the all-atom energy function. The AMBGMIN output contains averages over MD time steps which is not the same at the evaluation of the lowest energy state. One way of doing this is to run one step of minimisation with SANDER.

This is easily done. Three input files are needed prmtop, inpcrd, and mdin, along with the SANDER executable.

-> numreplicas

  (number of repilcas)

-> groupfile

   -A -i mdin.rep1 -o mdout.rep1 -c inpcrd.rep1 -p ./ala2.prmtop -r restrt.rep1 -x mdcrd.rep1 -inf mdinfo.rep1

The names of 'numreplicas' and 'groupfile' can not be changed! All other files you can name as you like.

mdin.rep*, inpcrd.rep* and ala2.prmtop define the other input files; all other files are for output.

The inpcrd.rep* and ala2.prmtop are the usual coordinate and topology files, and mdin.rep* define the input for the MD for each replica:

REMD run 1

&cntrl
       imin = 0, nstlim = 500, dt = 0.002,
       tempi = 0, temp0 = 100.0,
       ntt = 3, tol = 0.000001, gamma_ln = 5.0,
       ntc = 2, ntf = 1, ntb = 0, ntx = 5,
       ntwx = 500, ntwe = 0, ntwr =500, ntpr = 500,
       cut = 99.0, igb = 0, saltcon=0.0,
       nscm = 500, irest=1,
       ntave = 0, numexchg=100000
&end