AMBER: SHAKE failure in TI calculation of zero sum model system of "ethane-to-ethane" in water

From: Ye Mei <>
Date: Mon, 23 Jul 2007 21:00:34 +0800

Dear Amber community£¨

I wanted to repeat the work of David A. Pearlman published in J. Phys. Chem. 1994, 98, 1487 studying the zero sum model system of "ethane-to-ethane" in water. I built two parameter files corresponding to two ends (lambda=0 and lambda=1). Starting from the structure of lambda=0, I soaked it in a TIP3P water box with a buffer size 15 Angstrom, and then the whole complex was minimized, followed by heating up to 300K and 500ps constant temperature MD simulation.
Then I started the multisander to run TI calculation with icfe=2. But it died soon with error message in the output file related to lambda=1 as below:

     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 0 5 8 11

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

Is there anyway to fix it? Or must I disable SHAKE?
Related files are in the attachment.
Best regards,

Ye Mei, Ph.D.
Institute of Theoretical and Computational Chemistry
Key Laboratory of Mesoscopic Chemistry of MOE
School of Chemistry and Chemical Engineering
Nanjing University
Nanjing 210093

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Received on Wed Jul 25 2007 - 06:07:17 PDT
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