AMBER Archive (2009)

Subject: [AMBER] Appropriate nmode input file for gas and vacuum phase simulation

From: Scott Pendley (
Date: Fri Aug 07 2009 - 12:48:52 CDT

Hello everyone,

I am attempting to calculate the free energy of solvation for several small
organic molecules. I want to use nmode to calculate entropic contributions
in the gas phase (or vaccuum phase) and was having trouble finding a listing
of the variables that can be passed to the nmode program. I have modified
the input script from the MM-PBSA program slightly as follows

File generated by
  ntx = 0,
  ntrun = 1, nvect = 0,
  drms = 1000,
  dielc = 1.0, idiel = 1,
  scnb = 2.0, scee = 1.2,
  t = 298.0

The presence of external and internal dielectic variables suggests that
nmode would be operating under the assumption of continuum solvent which
would not be present in vacuum phase simulations. Any suggestions on
modifications to the input script or approaches to make this calculation?

Thank you,

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