Re: Self-Assemble Monolayer--Periodic Boundary Conditions

From: Natnael Doilicho (nbd_at_uchicago.edu)
Date: Wed Oct 01 2014 - 16:14:52 CDT

I am actually simulating a protein on the top of the surface. Do you know
what the effect of only adopting the pressure in Z axis may be on the
protein behavior?

Thanks for the reply,

Natnael Doilicho

On Tue, Sep 30, 2014 at 1:38 AM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:

> So you want to keep cell size in X and Y and only want to adapt pressure
> in Z?
>
>
>
> useflexiblecell yes
>
> useconstantarea yes
>
>
>
> Otherwise please explain more general.
>
>
>
> Norman Geist.
>
>
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Natnael Doilicho
> *Gesendet:* Dienstag, 30. September 2014 01:03
> *An:* namd-l_at_ks.uiuc.edu
> *Betreff:* namd-l: Self-Assemble Monolayer--Periodic Boundary Conditions
>
>
>
> Hi all,
>
>
>
> I am simulating an Alkanethiol Self-Assembled Mononlayer.
>
>
>
> The layer has at its base a hexagonally patterned plane of Sulfur atoms,
> each 5 Angstroms from one another.
>
>
>
> When I run the equilibration (under NPT conditions), the adjacent image
> cells move closer to the original, disturbing the 5 Angstrom exclusion
> distance between the sulfur atoms around the edges of the square system.
>
>
>
> Is there a way to limit or cease this universal contraction?
>
>
>
> Thanks,
>
>
> Natnael Doilicho
>
> University of Chicago
>
>
>
>
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