update:
something strange still happens during an equilibration :-)
I am doing NPT equilibration with berendsen barostat, during 10 ns
with the restrains on the protein's side-chains (its strength is
gradually decreased):
ntb=2, ! Constant pressure periodic boundary conditions
ntp=3, ! Semi-Anisotropic pressure coupling
pres0=1.0, ! Target external pressure, in bar
taup=0.5,
csurften=3,
gamma_ten=0.0,
ninterface=2,
Everything OK with the system, the area-per lipids in around 80
In the next 10 ns I continue to use the same protol of equilibration
but without of any restraints. From this point the system looks really
strange. It starts to change its dimensions rapidly along Z dimension,
the area per lipids is drooped to 60 and becomes stable. From the
visual perspective systems looks VERY elongated along Z (as compared
to GROMACS simulations or CHARM-gui based runs with CHARM36 ff of the
same system run in Amber).
Any suggestions?
James
2017-08-18 16:51 GMT+02:00 ABEL Stephane <Stephane.ABEL.cea.fr>:
> 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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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
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Received on Tue Aug 22 2017 - 07:30:03 PDT
