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 Tue Mar 05 2013 - 20:00:02 PST
