Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui

From: ABEL Stephane <>
Date: Fri, 18 Aug 2017 10:30:45 +0000

Hello James,

You have this error because of your membrane is not enough equilibrated . In my experience it may take a long time (>100 ns) to have a well equilibrated system if this this latter is constructed with CHARMM-GUI . So you could run a equilibration stage of your system, first in the NPAT ensemble during dozens ns, and switch to anisotropic ensemble (with lipid14) when you think (see the variations of the , x, y and z values vs. time) that you system is stable.

Good luck

De : James Starlight []
Envoyé : vendredi 18 août 2017 09:23
À : AMBER Mailing List
Objet : [AMBER] An equilibration of the membrane protein prepared by charmm-gui

Dear Amber Users!

I have followed Amber tutorial of the membrane protein modeling
embedded in Charmm-gui prepared membrane. On the 6ns of the
unrestrained equilibration my systems has been crashed with following

ERROR: Calculation halted. Periodic box dimensions have changed too
much from their initial values.

  Your system density has likely changed by a large amount, probably from

  starting the simulation from a structure a long way from equilibrium.

Looking on the system I have found that membrane thickness was
increasing along Z direction.

Question: how long equilibration should be for membrane protein
embedded in charmm-gui prepared membrane ? I have checked a charmm-gui
default protocol and found that the proposed equilibration is very
short. Also they introduce a restraints on the lipids during
equilibration. Is it useful approach to make it shorter?

Thanks !


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Received on Fri Aug 18 2017 - 04:00:02 PDT
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