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

Thu Apr 29 16:52:39 CEST 2010

Well 1 nm / 3 ns is definitely not reasonable! That is about 1 m /  
s ... 3.6 km/h

We has seen motion of the COM of a bilayer using CG models but the  
motions
were ~ 0.1 nm on the mircosecond timescale! This is due to the way COM  
is
removed ... not exact but appears only on large time scales.

On Apr 29, 2010, at 4:23 PM, ERIKSSON, EMMA wrote:

> The translation occurs in the z direction, yes. I'm running many  
> constrained simulations but in general the movement of the new  
> simulations, in which the COM translation has been removed for the  
> bilayer and water separately, is about 1 nm in 3 ns. The movement is  
> slower than when I was running the comm-grps = the whole system all  
> together, but the system will still end up crossing the pbc sometime  
> during 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]  
> f&#246;r XAvier Periole [x.periole at rug.nl]
> Skickat: den 29 april 2010 14:28
> Till: jalemkul at vt.edu; Discussion list for GROMACS users
> Ämne: Re: [gmx-users] Constrained simulations crash when bilayer  
> moves  in      the z direction in the box
>
> 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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>> --
>> ========================================
>>
>> 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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