Your restraint weights are very high. I'm not sure if the high
temperature is related. The output file ends before the SHAKE error as
seen in TextEdit/osx. Have you visualized the trajectory? I would try
weights of 1 and adjust/retry from there if that doesn't crash.
Bill
On 10/1/16 4:40 AM, ABHIJEET CHOWDHURY wrote:
> Dear AMBER users,
>
> I am trying to simulate a RNA duplex in an implicit solvent with igb=5
> but after some time into production, I get error saying
>
> " Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 2 233 677 678
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system."
>
> I am attaching the output file for more information. Can anyone
> suggest where to look for problem.
> PS: I had asked this question before but couldn't find that thread.
>
> Regards,
> Abhijeet Chowdhury
>
>
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Received on Sat Oct 01 2016 - 06:00:03 PDT
