RE: Question about "useConstantArea" in puresure control model

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Sat Apr 21 2018 - 13:49:08 CDT

It used to be that CHARMM27 didn't equilibrate to the right area per lipid if left to its own devices, and so it was common to combine CHARMM27 with a fixed area barostat to force the correct behavior. I think the membrane protein tutorial may reflect that history.

-Josh



On 2018-04-21 10:04:53-06:00 owner-namd-l_at_ks.uiuc.edu wrote:

Dear all
     I'm appling MD simulation of a membrane protein. But when reading the membrane protein tutorial, I found that the method "useConstantArea" was applied during the last step of the simulation, which limited the PBC could only change it's volume along z-axis. My queation is, would this happen in the real physiological-environment, and if this method has it's physiological significance ?
     Thanks a lot.


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