[AMBER] SMD free energy inferred from work

From: Ruth Helena Tichauer <rhtichau.laas.fr>
Date: Mon, 24 Sep 2018 15:46:42 +0200

Dear Amber users and developers,

I’m running SMD to evaluate the PMF of a reaction using the following input file:

SMD: LCOD rxn coord
  irest=1, ntx=5,
  ntb=2, pres0=1.0, ntp=1, taup=1.0,
  tempi=300.0, temp0=300.0,
  ntt=3, gamma_ln=2.0, ig=-1,
  nstlim=20000, dt=0.001,
  ntpr=20, ntwx=20, ntwr=5000, ioutfm=1,
  ntc=2, ntf=2,
  ifqnt=1, infe=1
  qmmask = ':169,196-199',
   output_file = 'nat_smd25-7.txt'
   output_freq = 20

And the cv_file:

  cv_type = 'LCOD'
  cv_ni=4, cv_i = 2947,2647,2650,2647,
  cv_nr=2, cv_r = 1.0,-1.0,
  npath=2, path = 2.26718,-1.9,
  nharm=1, harm = 25.0
I wonder which is the minimum number of trajectories that I should run and how to evaluate the PMF (is it just the arithmetic mean of all the values obtained for the total work done?).

Thank you in advance for any insight,


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Received on Mon Sep 24 2018 - 07:00:02 PDT
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