AMBER Archive (2008)

Subject: AMBER: rmsd vs frame

From: Francesco Pietra (
Date: Wed May 28 2008 - 17:56:24 CDT

In order to plot rmsd vs frame with reference to the lowest_potential_energy frame, I know the latter from ptraj as NSTEP = 195000 of prod5.out, which is the last production run out of five runs). reads:

  imin=0, irest=1, ntx=5,
  nstlim=333334, dt=0.0015,
  cut=10, ntb=2, ntp=1, taup=2.0,
  ntc=2, ntf=2,
  ntpr=1000, ntwx=1000,
  ntt=3, gamma_ln=2.0,

Is that correct 333334 x 4 = 1333336 + 195000 = 1528336 as the corresponding frame ?

Having the lowest energy in the last production run, I assume to be at a preliminary stage of the production. Correct?

francesco pietra

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