James,
There is not a general response. For instance you could do these steps
1) Equilibrate your system with position restraints applied on the protein only, say 50 - 100 ns in a semisotropic pressure
and check the x,y and z box length values. Are they stable ? if yes -> step 2. If not continue step 1
2) Equilibrated your system with NO position restraints, say 50 ns in a semisotropic pressure scheme and and check the x,y and z box length values. Are they stable? if yes -> step 3 . if not If not continue step 2
3) Equilibrated your system with NO position restraints, say 50ns of MD in anisotropic pressure and and check the x,y and z box length values. Are they stable ? If yes ---> you got it and you can start the production run. If not continue the step 2
HTH
Stéphane
________________________________________
De : James Starlight [jmsstarlight.gmail.com]
Envoyé : vendredi 18 août 2017 16:33
À : AMBER Mailing List
Objet : Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui
Hi Stephane,
how long the restraint are applied in you case on the protein (all
atoms and bb only) during the equilibration? As I have said, I noticed
the changing og the membrane thickness (correlated with an area per
lipid) only when I remove ALL posres from the protein ...
James
2017-08-18 16:28 GMT+02:00 ABEL Stephane <Stephane.ABEL.cea.fr>:
> 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 - 08:00:06 PDT
