* 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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>>
>>
>>
>> --
>> Amy Rice
>> Ph.D. Student
>> Physics Department
>> Illinois Institute of Technology
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Received on Thu Aug 31 2017 - 10:00:04 PDT
