Hi james
OK for the POPC
In case I have already constructed a membrane protein system but with much more POPC (403 molecules). The simulation were performed with GROMACS and by using Lipid14 for the POPC. So if you are interested i can send you a link for my parameters and you could try them with your system and see if you system still crashes. If yes, contact me directly
Stéphane
De : James Starlight [jmsstarlight.gmail.com]
Envoyé : vendredi 1 septembre 2017 15:08
À : AMBER Mailing List
Objet : Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui
Hello Stéphane,
Thank you so much for the message.
The simulation system shown on the movie is a very simple case:
it is 120 popc lipid, around 13.000 water and 1 GPCR.
The system has been prepared via Charmm-gui.
I have run a lot of GROMACS simulations of this system with Charmm36
force field as well as using Charmm36 and the system was very stable.
I don't really know why it take place in case of amber 14sb ff with
lipids14 because actually I am using very similar protocol of the
equilibration short nvt + npt with decreasing of restraints on the
protein. Is is an example:
GPCR equilibration 310K 125ns
&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=1,
tol=0.0000001, ! SHAKE tolerance
nstlim=500000, ! 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
ntp=3, ! Semi-Anisotropic pressure coupling
pres0=1.0, ! Target external pressure, in bar
taup=5.0,
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=1.0, restraintmask='.CA,C,O,N'
/
&ewald
skinnb=5, ! Increase skinnb to avoid skinnb errors
/
In next step just I set the restraint_wt=0.0 that collaps begin. BTW
even in those unpleasant picture the simulation is very stable, there
is no crash reports from amber.
Because I am using GPU code of pmemd.cuda. MB it is some bug of my
GPU?? I am using the old tesla card.
P.S. If you have any of you own GPCR system made for Amber you can
give me it and I will test it with my gpu machine...
2017-09-01 11:23 GMT+02:00 ABEL Stephane <Stephane.ABEL.cea.fr>:
> Hello James
>
> >From the movie I can see that the lipid patch around the protein is small. How many lipids you have used ? It is possible that the protein has a strong destabilization effect on the lipid around the protein. Did you try to increase the size of the lipid patch and rerun the simulation with the protein?
>
> Stéphane
>
>
> ________________________________________
> De : James Starlight [jmsstarlight.gmail.com]
> Envoyé : vendredi 1 septembre 2017 09:52
> À : jimkress_58.kressworks.org; AMBER Mailing List
> Objet : Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui
>
> - 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
>>>>> >>>>>>
>>>>> >>>>>> _______________________________________________
>>>>> >>>>>> AMBER mailing list
>>>>> >>>>>> AMBER.ambermd.org
>>>>> >>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>> >>>>>
>>>>> >>>>> _______________________________________________
>>>>> >>>>> AMBER mailing list
>>>>> >>>>> AMBER.ambermd.org
>>>>> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>> >>>>>
>>>>> >>>>> _______________________________________________
>>>>> >>>>> AMBER mailing list
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>>>>> >>>>
>>>>> >>>> _______________________________________________
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>>>>> >>>>
>>>>> >>>> _______________________________________________
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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 - 07:30:03 PDT
