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.
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.
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:
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.
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:21:01 CST