Re: Keep PBC box size in Z-direction constant?

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Wed Feb 22 2012 - 03:36:42 CST

On Tue, Feb 21, 2012 at 07:27, Norman Geist
<norman.geist_at_uni-greifswald.de> wrote:
> Hi,
>
> You can hold it only in XY with "useconstantarea", so you could simply rotate your box and let pressure happen in Z. The reason why your simulation crashes might be fixed atoms at the boundaries of the periodic box, which cannot be rescaled or something very similar. Often this error comes with fixed atoms. You could try to increase the relaxation time of the pressure control if you do not have fixed atoms at the boundaries, but inside the system, as sometimes it happens that the atom coordinate rescaling due to pressure, when happening in too big step, creates heavy forces when rescaling free atoms into fixed ones.
>
> Feel free to ask further.
>
> Good luck
>
> Norman Geist.
>
>

Hi Norman,

thanks for your suggestions, but I do not have any fixed atoms nor do
I apply any sort of constraints/restraints the only thing that is
fixing something is the SHAKE algorithm for Protons.
Here are some more details about the simulation:

+++++++++++++++
+Vacuum
+--------------------------+
+Lipid monolayer
+--------------------------+
+Water
+--------------------------+
+Lipid monolayer
+--------------------------+
+Vacuum
+++++++++++++++

What happens in a normal NPT or NPgT with flexible cell and constant
area or constant ratio simulation ist, that the PBC-box (+) shrinks in
Z direction and the vacuum area vanishes and the monolayers are
forming a perfect bilayer at ~100ns.

In the first ns the system runs fine, the solvent shrinks (a few
Ångström) to a perfect density. After that the system does not change
a lot.

I'll try your suggestion and increase LangevinPistonDecay and
LangevinPistonPeriod

I run out of ideas how to fix it except to switch the ensemble to NVT
but this would render the simulation incomparable to my other
simulations

Cheers,
Bjoern

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:24:46 CST