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

[XAvier Periole]

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 [gmx-users-bounces at gromacs.org]  
> för XAvier Periole [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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