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?
Interfacial systems such as membranes can translate independently of surrounding
aqueous solvent. Thus, the lipids could move one way, the water can move in the
other way, but overall, the net COM motion is zero. If you specify two groups,
as Xavier suggested, you treat the COM motion more appropriately. So, more
specifically:
comm-grps = DPPC_CHOL_MOL SOL
...replacing, of course, whatever your small molecule name where I have "MOL."
You will need a custom index group created by make_ndx to generate this first group.
-Justin
Sorry that I didn't understand you explanation.
Emma
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*Från:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org]
för XAvier Periole [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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