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-boun...@gromacs.org [gmx-users-boun...@gromacs.org]
för XAvier Periole [x.peri...@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-boun...@gromacs.org
<mailto:gmx-users-boun...@gromacs.org> [gmx-users-boun...@gromacs.org
<mailto:gmx-users-boun...@gromacs.org>] för XAvier Periole
[x.peri...@rug.nl <mailto:x.peri...@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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