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

XAvier Periole x.periole at rug.nl
Thu Apr 29 15:28:40 CEST 2010 

It is indeed not clear how you system may translate still! Is this  
translation on
the z axis? How much does it move and how quick?

On Apr 29, 2010, at 3:09 PM, Justin A. Lemkul wrote:

>
> 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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>>>
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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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