Unless I missed something, no model should be stable at 400k. Saying more
isn't possible Le without knowing more about what you want to learn and how
these 2 runs are designed to help that.
On Mar 5, 2013 10:31 PM, "Theodosia Teo" <theodosiaths.gmail.com> wrote:
> Dear Amber Users,
>
> I have developed two models for my protein kinase with different
> temperature; one at 400K and one at 1000K. I also used the exact same
> parameters for these two simulated models, with the exception that there is
> no constraint applied to the 400K whereas the 1000K-model has a constraint
> of 5.0 kcal mol-1 A-1 applied on the entire protein.
>
> After the 50 ns simulations, I am aware of the stability of the simulated
> models that I have built, so I checked for both their RMSD values. For the
> 1000K model, the RMSD fluctuates at around 9A throughout the simulation;
> however, for the 400K model, it fluctuates too much (it fluctuates from 3A
> to 9A within the first 20ns and drops to around 6A during the next 10 ns,
> and reaches the highest RMSD of 12A at 40ns). To my understanding, the 400K
> model that I have built is not stable at all.
>
> So i just wondering what can I do to have a more stable 400K-model? Does it
> means that a longer equilibration time is needed for the 400K model?
>
> Please help. Many thanks.
>
> Regards,
> T
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Received on Thu Mar 07 2013 - 03:30:02 PST
