AMBER Archive (2007)

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

From: Ye Mei (ymei_at_itcc.nju.edu.cn)
Date: Mon Jul 23 2007 - 08:00:34 CDT


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.
ymei_at_itcc.nju.edu.cn
Institute of Theoretical and Computational Chemistry
Key Laboratory of Mesoscopic Chemistry of MOE
School of Chemistry and Chemical Engineering
Nanjing University
Nanjing 210093
P.R.China
2007-07-23





  • application/octet-stream attachment: step1.in


  • application/octet-stream attachment: 0.prepc


  • application/octet-stream attachment: 1.prepc


  • application/octet-stream attachment: frcmod


  • application/octet-stream attachment: leap.in


  • application/octet-stream attachment: md2.rst




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