Hi Daniel Roe,
Thank you very much ur reply. I have attached the RMSD plots. I
measured that RMSD w.r.t the CA, C and N atoms. I have equilibrated
system for 2ns without constraints . The energy plots ande ensity
values seems to be the same...Do I need to extend my equilibration
stage?
Rajesh
On Fri, 8 Jul 2011 15:43:57 -0400
Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Fri, Jul 8, 2011 at 1:49 PM, Rajesh Raju
> <rajesh.raju.mail.chem.tamu.edu> 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
> again?
>
> -Dan
>
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Received on Fri Jul 08 2011 - 14:00:04 PDT
