Steered MD simulation in AMBER using Torsion as the reaction coordination.

I need to generate a set of trajectory of the rotation of one dihedral in a polymer. AMBERTOOLS14 has a command “dihedralscan” to do that, but it only works for dihedrals of proteins. It’s not allowed to define your own dihedral. So I chose SMD to do this.

It’s not complicated to set up the system. The only confusing part is the value of coordinate of torsion is rad not degree.

The input file of NPT part is listed below in case you might need. The initial torsion was about -1rad. To rotate 360degree. I set the reaction coordinate change from the initial value to 5.3. The diehdral is on residue 10 ( atom  100, 196, 155, 175). The rest parts are restrained with 500kcal/mol/angstrom^2.

NPT MD
 &cntrl
  imin = 0, irest = 1, ntx = 7,
  ntb = 2, pres0 = 1.0, ntp = 1,
  taup = 2.0,
  cut = 10.0, ntr = 1,
  ntc = 1, ntf = 1,
  tempi = 300.0, temp0 = 300.0,
  ntt = 3, gamma_ln = 1.0,
  nstlim = 100000, dt = 0.001,
  ntpr = 1000, ntwx = 1000, ntwr = 1000, ig = -1,
 /
Weak Hold
500.0
RES 1 9
RES 11 20
END
END

ncsu_smd
 output_file = 'smd.txt'
 output_freq = 1000
 variable
  type = TORSION
  i = (100, 196, 155, 175)
  path = (X, 5.3) path_mode = LINES
  harm = (100.0)
 end variable
end ncsu_smd
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