RE: Question about "useConstantArea" in puresure control model

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon Apr 23 2018 - 10:54:23 CDT

Right, which is why there is a "constantRatio" option, so that the membrane normal axes grow and shrink together. Semiisotropic barostats are pretty common for membrane systems, and decouple the water box from the membrane as best as possible.
-Josh

On 2018-04-23 06:38:45-06:00 Brian Radak wrote:

Isn't there also a problem with anisotropy in the PME calculation? That is, constant pressure may cause translational, rotational, and volume dependence of the potential (since the grid is expanding and contracting non-uniformly). This is presumably not so bad if the system itself is anisotropic, but one might reasonably expect that a fairly homogeneous membrane is in fact isotropic along the surface.

On Sat, Apr 21, 2018 at 2:49 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov<mailto:Joshua.Vermaas_at_nrel.gov>> wrote:
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<mailto: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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