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

From: Rajesh Raju <>
Date: Fri, 08 Jul 2011 15:16:48 -0500

Sorry I forgot to attahced the file...
n Fri, 8 Jul 2011 15:43:57 -0400
  Daniel Roe <> wrote:
> Hi,
> 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
> are seeing it's difficult to know how different things really are
> between the simulations. It is true that over a long enough
> 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)
> only 4 ns. I wouldn't even consider you out of the equilibration
> 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
> RMSD calculation? It's difficult to get an idea for what's really
> happening during your simulation - maybe try attaching your RMSD
> again?
> -Dan
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Received on Fri Jul 08 2011 - 13:30:04 PDT
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