- that begins only when I remove all posres from the protein
- there is nothing wrong with protein conformation
- on lipid-per-area plot the area estimated for POPC ( :OL) - the
graph dropped from 80 (only backbone posres are applied) to ~ 55 (no
posres) suddenly and becomes constant within this range.
2017-08-31 22:28 GMT+02:00 James Kress <jimkress_58.kressworks.org>:
> Doesn't look like "equilibration". Looks like explosion.
>
> Jim Kress
>
> -----Original Message-----
> From: James Starlight [mailto:jmsstarlight.gmail.com]
> Sent: Thursday, August 31, 2017 12:58 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui
>
> * for those who can not wait friday, the pilot version of the movie * https://youtu.be/DN0RzSQFUmQ
>
> 2017-08-31 18:31 GMT+02:00 James Starlight <jmsstarlight.gmail.com>:
>> Hi Amy,
>>
>> thank you so much for the message.
>>
>> 1- Assuming that without the receptor the same POPC bilayer looks very
>> stable under the same conditions
>>
>> 2- In charm36 ff the bilayer the same system looks very stable during
>> all of the simulation (I just have checked it on the system prepared
>> in charm-gui and run in Amber16)
>>
>> 3- Nothing happens with the conformation of the protein althought it
>> was simulated on a short timescales ~ 30 ns.
>>
>> Tomorrow a new *friday* movie will be available showing a strange
>> things of the lipids happened just after all the restraints from the
>> proteins were removed.
>>
>> James
>>
>>
>>
>> 2017-08-31 17:23 GMT+02:00 Amy Rice <arice3.hawk.iit.edu>:
>>> Hi James,
>>> I think it is unlikely that this is just a visualization issue. Which
>>> lipid type are you using? It looks to me like you could be
>>> experiencing a phase transition, something I've seen happen in my
>>> simulations with DPPE under similar simulation conditions. Have you
>>> tried simulating the bilayer without GPCR to see if the same behavior
>>> occurs? This would be my first step if you haven't done so already.
>>> You might also try simulating the system in AMBER using the C36 force
>>> field (very easy to convert charmm to amber with the chamber command
>>> in parmed) to see if this behavior is force field dependent or not.
>>> One last though- perhaps this bilayer thickening is an expected
>>> behavior. I haven't done much work with membrane-bound proteins, but
>>> I suspect a significant hydrophobic mismatch between the protein/bilayer could lead to a local bilayer thickening near the protein.
>>> To see if this is the case, I would simulate the protein in a larger
>>> bilayer patch, then use something like MEMBPLUGIN in VMD (
>>> https://sourceforge.net/p/membplugin/wiki/Home/) to see if local
>>> thickening is occurring. Hope this gives you some ideas!
>>> - Amy
>>>
>>> On Thu, Aug 31, 2017 at 9:52 AM, James Starlight
>>> <jmsstarlight.gmail.com>
>>> wrote:
>>>
>>>> update:
>>>>
>>>> :-)
>>>>
>>>> I have prepared another GPCR system and changed the equilibration
>>>> params with very big tau_p for equilibration period which was set
>>>> around 5ps. Visually the system looked the same - deformation of
>>>> the bilayer along the plane parallel to its normal, just after all
>>>> of the restrains were removed from the protein.
>>>>
>>>> MB it is some visualization issue due to the PBC artifacts ??
>>>> What commands for cpptraj I should provide to remove periodicity
>>>> correctly for the lipid-bilayer system?
>>>> Now I am just using: trjout trajectory.trr trr nobox which produce
>>>> such unpleasant picture.
>>>>
>>>>
>>>>
>>>> 2017-08-25 23:26 GMT+02:00 James Starlight <jmsstarlight.gmail.com>:
>>>> > 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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>>>> >>>>>
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>>>
>>>
>>>
>>> --
>>> Amy Rice
>>> Ph.D. Student
>>> Physics Department
>>> Illinois Institute of Technology
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Received on Fri Sep 01 2017 - 01:00:02 PDT
