AMBER: deeper problem with the energetics

From: Pankaj R. Daga <>
Date: Thu, 17 May 2007 08:46:33 -0500

Hi Amber community,

I am running a MD simulation with one homology model, I have built. For doing so, I have carried out four step minimization (Solvent, Hydrogen, Side-chain and Full), followed by two step heating (0-100 at constant volume, force const 20 and 100-300 at constant pressure, force const 10). Finally Three step equilibration each 100 ps at constant pressure with decreasing harmonic constraints (1, 0.1, and 0). All the precautions were taken to equilibrate the system properly.

When I am running the last equilibration step, I ended up in the error saying that SHAKE cannot be accomplished. Here is the error as follows. I have searched through the archives, for the similar problem. I found that these problems are mostly associated with harmonic constraints. In my case, I don't have any. Still I am facing this problem.

Can anybody suggest me, what the problem could be? I am attaching the input and output file along with.

Please help.



 vlimit exceeded for step 32333 ; vmax = 82.6417035434410

     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 2 3211 6561 6562

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

If your ship doesn't come in, swim out to it.......Jonathan Winters
Pankaj R. Daga |
Department of Medicinal Chemistry | e-mail:
417 Faser Hall, School of Pharmacy | fax: +1-662-915-5638
University of Mississippi | phone: +1-662-915-1853
University, MS, 38677-1848 |

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Received on Sun May 20 2007 - 06:07:22 PDT
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