From: Jeffrey J. Potoff (jpotoff_at_chem1.eng.wayne.edu)
Date: Thu Mar 13 2008 - 10:22:18 CDT
What is happening is that your system volume has changed significantly
during the course of the simulation. Look for the following problems:
1. Instability due to overlap of atoms, or other highly unfavorable
interactions. This will generate an enormous force; system blows apart.
2. System isn't equilibrated. Initial density is too high or too low.
Either way, if the simulation has to go a long way to get to the "correct"
density, you will get this error. As long as the system isn't flying
apart, you can restart from the final configuration and eventually will
get something stable where NAMD doesn't complain about the patch grid.
On Wed, 12 Mar 2008, List wrote:
> Dear NAMD experts,
> I have some questions about FEP (Free Energy Perturbation) and MCTI (Thermodynamic Integration). The configuration file I used is attached. Here are my questions:
> 1) I'm running FEP simulation in NPT ensemble. My system is a protein with a small water box enclosing the site of interest, and I'm running non-PBC FEP with atoms far away from that site fixed. According to some early posts in NAMD mailing list, I have the following settings:
> wrapAll off
> wrapNearest off
> PME no
> (All cellBasisVector1, ..., celOrigin lines have been removed)
> margin 2.5
> useFlexibleCell no
> But the FEP simulation CRASHED with the following error:
> FATAL ERROR: Periodic cell has become too small for original patch grid!
> Possible solutions are to restart from a recent checkpoint,
> increase margin, or disable useFlexibleCell for liquid simulation.
> I even tried to increase margin to a much bigger number but it didn't help. I'm not using PME/PBC, so I don't understand why it complains about the periodic cell. Could someone help?
> 2) I also tried NVE ensemble, but I got the message saying that FEP only works for NPT. Is this right?
> 3) In the FEP, I want to do thermodynamic integration, so I included the MCTI block in the configuration file AFTER the FEP specification. I wonder if this would work.
> Any help will be greatly appreciated.
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Jeffrey J. Potoff jpotoff_at_chem1.eng.wayne.edu
Associate Professor Wayne State University
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr Phone:(313)577-9357
Detroit, MI 48202 Fax: (313)578-5815
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