[AMBER] Jarzynski SMD

From: George Tzotzos <gtzotzos.me.com>
Date: Fri, 17 Oct 2014 16:39:19 -0300

Iím trying to explore possible pathways for the exit of a ligand from the binding pocket of its receptor.

Iíd appreciate any advice on the procedure that Iím following, which is as follows:

1. plan to repeat each SMD simulation 3-4 times from different starting coordinates taken from a 20ns MD trajectory. Is the number of repeats adequate?

2. Iím changing the distance of the centre of mass of my ligand to that of 10-14 residues in the proximity of the original position of the ligand in 1 Angstrom increments. Is incremental change of distance between the centers of mass of 1 Agstrom OK?

3. Iíve set rk2 = 500. Is this force acceptable?

Iíd be most grateful for any comments on the 3 questions above as well as my smd input file below.

Thank you in advance


My pushing input is

  cut=8.0, ntb=2, ntp=1, taup=2.0,
  ntpr=5000, ntwx=5000, ntwr=5000,
  ntt=3, gamma_ln=2.0, ig=-1,
&wt TYPE='DUMPFREQ', istep1=1, /
&wt TYPE='END', /
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Received on Fri Oct 17 2014 - 13:00:02 PDT
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