[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 15:39:12 CEST 2010 

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.

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
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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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