AMBER Archive (2009)

Subject: [AMBER] problem with the results in the .out file!

From: Aravind S (amm07bi007_at_students.amrita.ac.in)
Date: Tue Mar 31 2009 - 00:30:57 CDT

Dear Users,
I am facing another problem with my simulation.
I was trying to simulate 227d.pdb with the following parameters: there are no constraints involved. I ran the 50 ps simulation with a 10fs time step, temp remaining constant at 300K. By default my ntx=7 and irest=1. My .rst file used was the result got through my previous simulation.
My problem is that the .rst file isnt being generated , only the .mdcrd and the .out files got generated and the .mdcrd files had nothing written on it.
The error in the .out file showed in the results section...
the error read:--- Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 2 5 19 21

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.

I would be highly obliged if somebody could solve this problem of mine.
thank you

Aravind

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