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: [email protected]
[[email protected]] för Justin A. Lemkul [[email protected]]
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:
[email protected] [[email protected]] för
Justin A. Lemkul [[email protected]] 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:
[email protected] [[email protected]] för
Justin A. Lemkul [[email protected]] 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:* [email protected] [[email protected]]
för XAvier Periole [[email protected]] *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:* [email protected]
<mailto:[email protected]> [[email protected]
<mailto:[email protected]>] för XAvier Periole
[[email protected] <mailto:[email protected]>] *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 [email protected]
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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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