From: Brian Radak (brian.radak_at_gmail.com)
Date: Mon Apr 23 2018 - 11:20:26 CDT
Ah, yes, I conflated the two. My previous comment can be disregarded -
Thanks Josh.
On Mon, Apr 23, 2018 at 11:54 AM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:
> 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>
> 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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