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
>>>>
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Received on Wed Aug 23 2017 - 09:00:03 PDT
