[gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

ERIKSSON, EMMA E.ERIKSSON1 at nuigalway.ie
Thu Apr 29 16:40:12 CEST 2010 

The increase in z box length is due to that I have replaced 12 DPPC lipids by cholesterol molecules. Cholesterol reduces the area per lipid and compresses the bilayer lateral (xy) area, resulting in a slight increase in the water layer thickness. I have performed exactly the same simulations with a higher concentration of cholesterol (in which the bilayer is even more compressed and the water phase therefore is even thicker) and there is no translation in any of the simulations.


Emma Eriksson
PhD student in biophysical chemistry
School of chemistry
National University of Ireland - Galway
Galway, Ireland
________________________________________
Från: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] för Justin A. Lemkul [jalemkul at vt.edu]
Skickat: den 29 april 2010 15:28
Till: Gromacs Users' List
Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves  in      the z direction in the box

ERIKSSON, EMMA wrote:
> The last section of my mdp file:
>
> pull                     = constraint pull_geometry            = cylinder
> pull_r1                  = 1.0 pull_r0                  = 1.5 pull_group0
> = DPPC pull_group1              = MOL pull_vec1                = 0 0 1
> pull_init1               = 3.083
>
> comm_mode                = linear nstcomm                  = 1 comm_grps
> = DPPC_CHOL_MOL SOL
>
> With my small molecule being MOL. I'm constraining the distance between the
> DPPC and the small molecule at different distances along the z direction of
> the bilayer. This example is for the distance being 3.083 nm between the two
> groups. The total z box length is ~7.2 nm. Even when I'm running without
> constraint the system is translating in the z direction but no crash occurs
> when the pbc is crossed.
>

At this point, it would probably be useful to understand how you set up and
build the system.  The original 128-lipid DPPC from Tieleman is ~6.5 nm in the
z-dimension, so somewhere along the way you've picked up 0.7 nm.  Is there void
space in your box?  Did you remove the water and re-solvate?

There is no reason (in my mind) why the bilayer should be translating in the
z-dimension at all.  I've done a number of simulations with this particular DPPC
bilayer and never had a problem.  Maybe you can also post your whole .mdp file
to see if there are any problems.

-Justin

> Emma Eriksson PhD student in biophysical chemistry School of chemistry
> National University of Ireland - Galway Galway, Ireland
> ________________________________________ Från: gmx-users-bounces at gromacs.org
> [gmx-users-bounces at gromacs.org] för Justin A. Lemkul [jalemkul at vt.edu]
> Skickat: den 29 april 2010 14:33 Till: Gromacs Users' List Ämne: Re:
> [gmx-users] Constrained simulations crash when bilayer moves  in      the z
> direction in the box
>
> ERIKSSON, EMMA wrote:
>> My system consists of 128 lipids and 3655 water molecules and is one of the
>> structures one can download from University of Calgary. I think that the
>> water phase is thick enough because when I run non-constrained simulations
>> and the system translates there is no crash when the lipids cross the pbc.
>>
>
> What type of pulling are you trying to do?  Can you post your .mdp file, or
> at least your pull parameters?  My sense is that your pull distance is
> greater than half the box dimension in the pull direction, causing lipids to
> be pulled across PBC and break down.
>
> -Justin
>
>> Emma
>>
>>
>> ________________________________________ Från:
>> gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] för
>> Justin A. Lemkul [jalemkul at vt.edu] Skickat: den 29 april 2010 14:09 Till:
>> Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained
>> simulations crash when bilayer moves  in      the z direction in the box
>>
>> Do you have sufficient water on either "side" of your membrane?  That is,
>> are the lipids crossing PBC because of spurious interactions with the other
>> side of the membrane?  That would certainly be a reason for a crash - the
>> model physics is breaking down.  How did you generate your initial membrane
>> configuration?
>>
>> -Justin
>>
>> ERIKSSON, EMMA wrote:
>>> Hi again, I thought your suggestions would work for my membrane, but it
>>> seems like the removal of COM translation of the bilayer and water
>>> separately does not stop the system from translating in the box. My new
>>> simulations are now soon crashing again since the lipids are crossing the
>>> pbc. I was using two comm-grps, one containing DPPC_CHOL_MOL and one with
>>> water. How is it possible that the system still is able to translate? Is
>>> there any other way to do this? Otherwise I have to manually translate
>>> the system back to its original position in the box after the simulation
>>> has crashed and then continue the simulation, but this is not very good
>>> since I cannot use the checkpoint file then and the continuation is not
>>> exact. Any suggestion what to do? Thanks in advance.
>>>
>>> Emma
>>>
>>>
>>> ------------------------------------------------------------------------
>>> *Från:* gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] för
>>> XAvier Periole [x.periole at rug.nl] *Skickat:* den 27 april 2010 16:32
>>> *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users]
>>> Constrained simulations crash when bilayer moves in the z direction in
>>> the box
>>>
>>>
>>> you should remove the water and lipid bilayer COM separately. I am not
>>> sure what you should do with your small molecule though. Probably best to
>>> add it to the bilayer as you constrain their relative position!
>>>
>>> On Apr 27, 2010, at 4:32 PM, ERIKSSON, EMMA wrote:
>>>
>>>> Hi again, Thanks Xavier for your reply. I didn't know that this mdp
>>>> option existed. However, I read the manual and also checked the
>>>> mdout.mdp files for my previous simulations, and I understood it as if
>>>> those are the default settings even if you don't specify any of them in
>>>> the md.mdp file. The default comm_groups is the whole system so I guess
>>>> if I'm not writing anything there it will take the whole system. In
>>>> that case I think that in my previous simulations the translational
>>>> motion should have been removed for the whole system, but since it's
>>>> obviously not remove something is wrong. Or did I misunderstand
>>>> everything? My system consists of DPPC lipids, cholesterol, water and
>>>> one small molecule. Should I specify comm_groups as only the lipids? In
>>>> that case I get a warning from grompp. You wrote comm-grps = membrane
>>>> solvent + ions. Only the water then? Sorry that I didn't understand you
>>>> explanation.
>>>>
>>>> Emma
>>>>
>>>>
>>>> ------------------------------------------------------------------------
>>>>  *Från:* gmx-users-bounces at gromacs.org
>>>> <mailto:gmx-users-bounces at gromacs.org> [gmx-users-bounces at gromacs.org
>>>> <mailto:gmx-users-bounces at gromacs.org>] för XAvier Periole
>>>> [x.periole at rug.nl <mailto:x.periole at rug.nl>] *Skickat:* den 27 april
>>>> 2010 12:41 *Till:* Discussion list for GROMACS users *Ämne:* Re:
>>>> [gmx-users] Constrained simulations crash when bilayer moves in the z
>>>> direction in the box
>>>>
>>>>
>>>> The crash seems to be expected as by crossing the pbc the distance will
>>>> change significantly and in way the algorithm can not handle.
>>>>
>>>> Note that the overall translational motion of your system should always
>>>> be removed.
>>>>
>>>> The removal of the COM motion of your bilayer should be sufficient to
>>>> prevent the overall motion of the bilayer. have a look at the following
>>>> option in the mdp: ; mode for center of mass motion removal comm-mode
>>>> = Linear ; number of steps for center of mass motion removal nstcomm
>>>> = 1 ; group(s) for center of mass motion removal comm-grps
>>>> = membrane solvent+ions
>>>>
>>>>
>>>> On Apr 27, 2010, at 12:07 PM, ERIKSSON, EMMA wrote:
>>>>
>>>>> Hi all!
>>>>>
>>>>> I have a problem regarding lipid bilayer simulations in Gromacs 4.
>>>>> During some of my simulations the whole system is moving in the z
>>>>> direction in the box, meaning that after some time the lipids are
>>>>> going out in the bottom of the box and coming in in the top of the
>>>>> box, since I'm using periodic boundary conditions. This doesn't
>>>>> matter (I think) when running non-constrained simulations, however
>>>>> when I'm constraining the distance between the lipids
>>>>> (pull_geometry=cylinder) and a molecule in the system the system
>>>>> explodes and the simulations crash when the lipids are starting to
>>>>> cross over to the other side. The fact that the system is moving in
>>>>> the box must be the problem since the system explodes exactly when
>>>>> the first lipid passes over to the other side and nothing like this
>>>>> ever happens when the bilayer is not moving in the box. Is there any
>>>>> way to freeze the cylindrical COM of the lipids or something like
>>>>> that so that they stay more or less in the middle of the box all the
>>>>> time? I don't want to use freezegrps and freezedim = N N Y as this
>>>>> freezes the lipids completely in the z direction, and that's not what
>>>>>  I want, I want them to be free to move as before but I want to stop
>>>>> the whole system from moving too much in the z direction. Anyone that
>>>>>  has experienced a similar problem or know how to go about with this?
>>>>>  I would really appreciate any help I can get. Thanks.
>>>>>
>>>>> Emma -- gmx-users mailing list    gmx-users at gromacs.org
>>>>> <mailto:gmx-users at gromacs.org>
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>> -- ========================================
>>
>> Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee
>>  Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu
>> | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
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>
> -- ========================================
>
> Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee
> Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu |
> (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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