From: Jiao, Dian NMN (-EXP) (dnjiao_at_sandia.gov)
Date: Tue Sep 13 2011 - 12:45:50 CDT
I built this system with an ion channel embedded in POPC lipid layer (just followed the tutorial on setting up NAMD for membrane protein). Then I started to equilibrate the system. According to the tutorial, I need to fix the everything but the lipid tails to relax them at first. The conf file is pretty much the same as the example file. After a while, the run stopped due to the following error:
ERROR: Constraint failure in RATTLE algorithm for atom 14843!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely; see error messages above.
Atom 14843 is a lipid carbon. I can't tell what is wrong with that particular atom by looking at the structure. I thought it must have to do with the constraints, so I completely removed the constraints of lipids and kept the protein fixed and ran minimization again. The job died again due to the same type of error but different atom 14851. These two atoms are on the same lipid and very close to each other. What is causing the problem? Is that single lipid molecule that is messing up?
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