From: Arthur Oliveira Vale (arthurovale_at_uchicago.edu)
Date: Sun Jun 18 2017 - 20:14:32 CDT
In my research group we have a hypothesis that a protein may spontaneously disrupt a membrane and enter it. We would like to see this phenomenon (if at all a real phenomenon) happening in an MD simulation. We've being doing membrane simulations for quite sometimes, and we are aware that options such as useConstantArea and useConstantRatio may be used for those. Our issue is, due to the periodic conditions, we think that if we useConstantArea as set to yes then a hole will never spontaneously form in the membrane, because of the infinite bilayer (that is, if a lipid tries to move, another takes its place due to need to preserve area). So we were wondering if anyone has any thoughts on how to set up a configuration file for a namd simulation so that a hole may spontaneously form in a lipid bilayer.
Thank you in advance,
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