[AMBER] Simulation time help

From: Nicole Ippolito <ippolito.nicole89.gmail.com>
Date: Thu, 12 Dec 2013 10:28:31 -0600


I am trying to run a 1ns simulation for a total of 10ns; however, when I
did the RMSD it showed a simulation of 50ns total. I am unsure at this
point of what I am doing wrong and am having a hard time understanding how
the output works. I have looked at the tutorials and the manuals but am
still confused. Below is the in file:

  nstlim=1000000, dt=0.001, ntx=5, irest=1, ntpr=1000, ntwx=1000,
  temp0=300.0, ntt=1, tautp=2.0, ig=-1,
  ntb=1, ntp=0,
  ntc=2, ntf=2,
  cut=12.0, iwrap=1,

Any explanation would be greatly appreciated.

Thank you for your time,
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Received on Thu Dec 12 2013 - 08:30:02 PST
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