Re: [AMBER] Simulation time help

From: Adrian Roitberg <>
Date: Thu, 12 Dec 2013 11:30:49 -0500


First, I am confused about "run a 1ns simulation for a total of 10ns"

Second, how do you know that shows 50 ns in the rmsd plot? The rmsd plot
only looks at the frames in the dynamics file, and has no time
information per se.

On 12/12/13 11:28 AM, Nicole Ippolito wrote:
> Hello,
> 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:
> &cntrl
> 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,
> &end
> Any explanation would be greatly appreciated.
> Thank you for your time,
> Nicole
> _______________________________________________
> AMBER mailing list

                             Dr. Adrian E. Roitberg
Colonel Allan R. and Margaret G. Crow Term Professor.
Quantum Theory Project, Department of Chemistry
University of Florida
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Received on Thu Dec 12 2013 - 09:00:02 PST
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