Re: [AMBER] Different trajectories with different RMSD with changing the parameters of gamma_ln, taup, timesteps and extend of density equilibration

From: Daniel Roe <>
Date: Fri, 8 Jul 2011 15:43:57 -0400


On Fri, Jul 8, 2011 at 1:49 PM, Rajesh Raju
<> wrote:
> to the minimized structure after minimzation step2 (RED lines).. I
> have attached the RMSD plots. The RMSD plots shows a large variation

There were no plots attached to your mail (at least none that reached me).

> My questions:
> If these trajectories differ by changing the simulations parameters,
> how we can trust these results?
> Is there any 'best parameters for gamma_ln and taup.
> Is there any problems in the MD protocol which I followed?
> What is the reason for the odd behaviour in the RMSD plots and what
> should I do to get a stable MD trajectory?

Without seeing your plots or having some idea of what RMSD values you
are seeing it's difficult to know how different things really are
between the simulations. It is true that over a long enough timescale,
the average properties of 2 separate simulations done with similar
conditions should converge, but I would bet that you do not have
converged simulations of a large protein-DNA system (with ~400
residues I'm guessing a couple thousand atoms w/ explicit solvent) in
only 4 ns. I wouldn't even consider you out of the equilibration phase
at that point. Have you plotted your energy vs time? Is it stable?
What about your density? Has it reached a stable value during your
equilibration phase, or is it still changing? What makes you sure
that your trajectory is not stable - what atoms are you using in your
RMSD calculation? It's difficult to get an idea for what's really
happening during your simulation - maybe try attaching your RMSD plots


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Received on Fri Jul 08 2011 - 13:00:03 PDT
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