up:
so the proposed solutions to resolve the problem of lipid
equilibration shown on the video:
- increase time of the restrained simulation to allow lipids better
pack around the protein
- change tau_t or tau_p constants.
E.g in Langevin's dynamics lower tau_t should give more stabile system
(because we increase the friction which should be = mass/ tau_t)
What's about tau_p for berendsen barostat?
P.S. Does the GPCR inserted good in the membrane? Here I did it via
Charm-gui prediction a position of receptor within the lipids from OPM
data-base.
James
2017-08-23 17:50 GMT+02:00 James Starlight <jmsstarlight.gmail.com>:
> I make visualization of the problem in form of movie
> https://youtu.be/ImgtLtV3Yk4
>
> here what I have described in the previous post happens after 5 sec
> of the movie at the moment when all restraints are released from the
> protein.
> During the first part of the movie only the backbone are restrained.
>
> It looks like some option set wrong like compressibility or pressure
> along XY dim for semi-anisotropic coupling or something else ?
>
> Here the params of the simulation:
>
>
> &cntrl
> imin=0, ! Molecular dynamics
> ntx=5, ! Positions and velocities read formatted
> irest=1, ! Restart calculation
> ntc=2, ! SHAKE on for bonds with hydrogen
> ntf=2, ! No force evaluation for bonds with hydrogen
> ntr=0,
> tol=0.0000001, ! SHAKE tolerance
> nstlim=5000000, ! Number of MD steps
> ntt=3, ! Langevin dynamics
> gamma_ln=1.0, ! Collision frequency for Langevin dyn.
> temp0=310.0, ! Simulation temperature (K)
> ntpr=5000, ! Print to mdout every ntpr steps
> ntwr=5000, ! Write a restart file every ntwr steps
> ntwx=5000, ! Write to trajectory file every ntwc steps
> dt=0.002, ! Timestep (ps)
> ntb=2, ! Constant pressure periodic boundary conditions
> barostat=1,
> 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,
> cut=10.0, ! Nonbonded cutoff (Angstroms)
> ioutfm=1, ! Write binary NetCDF trajectory
> ntxo=2, ! Write binary restart file
> iwrap=1,
> restraint_wt=0.0, restraintmask='.CA,C,O,N'
> /
> &ewald
> skinnb=5, ! Increase skinnb to avoid skinnb errors
> /
>
> 2017-08-22 16:26 GMT+02:00 James Starlight <jmsstarlight.gmail.com>:
>> 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
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
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>>>>> AMBER mailing list
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>>>>> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri Aug 25 2017 - 14:30:02 PDT
