If you simulate complexes, make sure to look at the imaging commands. But
that probably isn't the case here. I would look carefully at your
equilibration protocol, which you did not tell us. A good protocol often
consists of multiple steps, including minimization, heating, use of
restraints and more. The details depend on the source of your structure, if
all atoms were well resolved, and more.
Since we can't really design a good protocol for your system, I suggest
looking at papers where people do careful equilibration on systems similar
to yours, with similar challenges. Adapt their protocol.
If you do decide to ask here for more help, tell us more about your initial
structure,and all of the details of each step of your equilibration.
On Mar 11, 2016 8:41 PM, "Arati Paudyal" <apsilwal123.gmail.com> wrote:
> Dear all,
>
> I just finished a 1 ns heating and a 60 ns production simulation. But when
> I processed the RMSD I feel like it is too high. I know the fluctuation
> from 1-3 angstron is expected but mine looks like it is over 4 sometimes.
> Could you please explain what might have gone wrong during simulation? IS
> there anything I can do to avoid such fluctuation during simulation? I
> used exactly same input and time to run another simulation with a different
> protein complex and rmsd was a lot lower in that case. I know it depends on
> the system but if I could understand if there is anything I can do to
> improve this it would be of great help. Can I even use any of these frames
> to process mmpbsa script?
>
> Rmsd input:
>
> trajin heat.rmsd
> trajin equil.rmsd
> reference x.inpcrd
> rms reference out backbone.rmsd .CA,C,N
>
>
> [image: Inline image 1]
>
>
> If I remove equil.mdcrd an donly do trajin heat.mdrcd, rmsd is alot lower
> but I can see it is increasing towards the end. So I think it is
> fluctuating more during equilibrium stage. Following is the one only with
> heat.mdcrd
>
>
> [image: Inline image 2]
>
>
>
>
> Thank you all in advance for your time!!!
>
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>
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Received on Fri Mar 11 2016 - 18:00:07 PST
