[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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