Re: Simulating Protein Entering membrane

From: Vermaas, Joshua (
Date: Mon Jun 19 2017 - 12:01:45 CDT

Hi Arthur,

Yeah, that would be my intuition too. What is wrong with constantratio? Constantarea was only needed for force fields pre-CHARMM36 that didn't get surface areas right. As a warning, the timescales will probably not be in your favor to do this atomistically. Just getting lipids out of the way for peripheral membrane protein insertion takes ages, so I'd expect this to work better at a coarse-grained level, since you don't actually care about protein structural changes.


On 06/18/2017 07:19 PM, Arthur Oliveira Vale wrote:
Dear all,

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,

Arthur Vale

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:22 CST