Thanks, Stéphane!
Yep, the Charm-gui protocol for AMBER (using Charmm params) also
proposes usage of Anisotropic scaling for equilibration and prod.runs.
Also Charm-gui proposes to use MC barostat (as opposed to Berendsen
which I am always using).
The questions -
1)Might the semi-anisotropic scaling with Berendsen thermostat (like
proposed in Tutorial) be more stable for the equilibration of the
membrane made via Lipid14 ?
2) Is it correct to turn off all restraints on the protein during
equilibration? I have noticed that membrane start to change its
dimensions just after I realize all restraints from the protein (or
apply only very weak on the side-chains).
Regards,
James
2017-08-18 12:30 GMT+02:00 ABEL Stephane <Stephane.ABEL.cea.fr>:
> 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
>
> Stéphane
> ________________________________________
> De : James Starlight [jmsstarlight.gmail.com]
> 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:
>
> 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 !
>
> James
>
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Received on Fri Aug 18 2017 - 07:00:04 PDT
