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

Justin A. Lemkul jalemkul at vt.edu
Thu Apr 29 16:28:33 CEST 2010 


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> 
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the
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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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