Re: Lipid bilayer equilibration: Periodic cell has become too small for original patch grid!

From: Bjoern Olausson (
Date: Wed Aug 10 2011 - 02:49:01 CDT

On Tuesday 09 August 2011 00:20:56 Andres Morales N wrote:
> Hi Bjoern
> I did not use Periodic Boundary Conditions in the equilibartion script
> because I use "extendedSystem dppc_cal300.xsc". First I minimized the
> system, then I heated it to 300 K. "dppc_cal300.xsc" is the xsc output
> file obtained from heating.
> Exactly what do you mean with "restart files to continue from"?
> Thanks for your help.

Sorry, I have overlooked the "extendedSystem" in your config.
But you might want to try to set the PBC manually and increase the box
dimensions slightly (compared to those from the xsc file).

If this doesn't help, you could try to restart your simulation from the crash
point. If it sill crashes after a few restarts, you should check your
structure and run a test in NVT.

Playing with the margin never helped me and in most cases there was either a
problem with the structure or I made a typo when setting the PBC (10.0 instead
of 100.0 or something similar).

Also you should visualize your structure. Use VMD and draw the PBC box. Then
you can see if your system grows unnaturally much.


Bjoern Olausson
Martin-Luther-Universitšt Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

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