[gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
ERIKSSON, EMMA
E.ERIKSSON1 at nuigalway.ie
Thu Apr 29 17:08:29 CEST 2010
Justin, you understood it correctly; I only have problems with the low cholesterol concentration.
According to g_traj -com the COM of DPPC in one of the simulations moves 0.6 nm in 3.5 ns. And as Xavier just wrote it's quite much...
My mdp file looks like this:
title = dppc128
cpp = /lib/cpp
include =
define =
integrator = md
dt = 0.002
nsteps = 3500000 ; 7 ns
nstlog = 25000
nstenergy = 25
nstxout = 750000
nstxtcout = 400
nstvout = 750000
nstfout = 0
xtc_grps = DPPC SOL CHOL MOL
energygrps = DPPC SOL CHOL MOL
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = Cut-off
rvdw = 1.0
tcoupl = Nose-hoover
tc-grps = DPPC SOL CHOL MOL
tau_t = 0.1 0.1 0.1 0.1
ref_t = 323 323 323 323
Pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 1.0 1.0e-14
compressibility = 4.5e-5 4.5e-15
ref_p = 1.0 1.0
gen_vel = yes
gen_temp = 323
gen_seed = 173529
constraints = all-bonds
pbc = xyz
optimize_fft = yes
unconstrained_start = no
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 = 3.498
comm_mode = linear
nstcomm = 1
comm_grps = DPPC_CHOL_MOL SOL
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 15:44
Till: Gromacs Users' List
Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
ERIKSSON, EMMA wrote:
> The increase in z box length is due to that I have replaced 12 DPPC lipids by
> cholesterol molecules. Cholesterol reduces the area per lipid and compresses
> the bilayer lateral (xy) area, resulting in a slight increase in the water
> layer thickness. I have performed exactly the same simulations with a higher
> concentration of cholesterol (in which the bilayer is even more compressed
> and the water phase therefore is even thicker) and there is no translation in
> any of the simulations.
>
So if I understand correctly, you have different levels of cholesterol in DPPC,
and at low cholesterol concentration you get a z-translation of your membrane,
but at high concentration of cholesterol, you get no translation at all? Can
you plot (using g_traj -com) the motion of the membrane to quantify just how
much the membrane is moving? And again I would ask that you post your entire
.mdp file, just to see your settings.
-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 15:28 Till: Gromacs Users' List Ämne: Re:
> [gmx-users] Constrained simulations crash when bilayer moves in the z
> direction in the box
>
> 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
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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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--
========================================
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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