[AMBER] Independent production runs

From: Lizelle Lubbe <LBBLIZ002.myuct.ac.za>
Date: Fri, 20 Oct 2017 11:28:34 +0000

Hi All,

I am aiming towards 30ns of production dynamics and have been advised to repeat this 3 times to demonstrate data reproducibility but am not sure how.
As suggested in the manual, I've used ig=-1 throughout heating, equilibration and production - is this correct?

Here's the input file for the first section of production, restarting from equilibration.rst7 and reading its velocities.

First Dynamic Simulation with Constant Pressure

 # Control section
  imin = 0,
  irest = 1,
  ntx = 5,
  ntb = 2, ntp = 1, pres0 = 1.0, taup = 1.0,
  cut = 10.0,
  ntc = 2, ntf = 2,
  temp0 = 300.0,
  ntt = 3, gamma_ln = 2, ig = -1,
  nstlim = 500000, dt = 0.002,
  ntwx = 5000, ntpr = 5000, ntwe = 5000, ntwr = -100000,
  ioutfm = 1,
  iwrap = 1,
  ntr = 0,
  ntwprt = 0,
  nmropt = 1,
  &wt type = 'END'/

There's a wall-clock time-limit on our HPC so the simulations were restarted each time using the input given above until the desired trajectory length was reached (always irest=1, ntx=5 and ig=-1).

I don't really understand the concept of MD reproducibility very well... Could someone please explain this to me?

Currently, I can think of two ways for restarting the production but don't know which is correct:
1. using ig=-1, irest=0, ntx=1 and starting from the same initial equilibrated coordinates as used for the first production
2. using ig=-1, irest=0, ntx=1 but starting from the rst7 file saved at 10ns for the second and 20ns for the third repeat production

Would option two demonstrate data reproducibility or just explore more conformational space (or are they the same thing)?
Is something like 30ns generally acceptable thesedays to investigate the motion of glycans and protein breathing or should it be increased?

Kind regards

Lizelle Lubbe

PhD (Medical biochemistry) candidate
Department of Integrative Biomedical Sciences
University of Cape Town
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Received on Fri Oct 20 2017 - 04:30:02 PDT
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