Re: Question about "useConstantArea" in puresure control model

From: Brian Radak (brian.radak_at_gmail.com)
Date: Mon Apr 23 2018 - 07:38:42 CDT

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>
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 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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