Hi James,
In general I use the Berendsen barostat in my MD during the first stage of the equilibration stage since it more stable and then switch to MC barostat when the system is stable.
As I said, it is preferable to perform the equilibration stage in semisotropic pressure to obtain a well equilibrated system and switch to anisotropic pressur when you system is stable It is particularly if the initial configuration of the system is not really good ( CHARMM-GUI). Keep in mind that was initially create for doing simulations with CHARMM and not Amber.
> 2) Is it correct to turn off all restraints on the protein during equilibration?
Depend of the system. But in general I restrain the protein at the beginning of the equilibration stage and then remove the restrain, when your system seems to be well equilibrated and then redo an equilibration without restrain
HTH
Stephane
________________________________________
De : James Starlight [jmsstarlight.gmail.com]
Envoyé : vendredi 18 août 2017 15:36
À : AMBER Mailing List
Objet : Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui
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 - 07:30:07 PDT
