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] [[email protected]]
för XAvier Periole [[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
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