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-boun...@gromacs.org [gmx-users-boun...@gromacs.org]
för XAvier Periole [x.peri...@rug.nl]
Skickat: den 29 april 2010 14:28
Till: jalem...@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
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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
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*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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