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: gmx-users-boun...@gromacs.org
[gmx-users-boun...@gromacs.org] för Justin A. Lemkul [jalem...@vt.edu]
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:
gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] för
Justin A. Lemkul [jalem...@vt.edu] 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:* 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 -- gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the
archive at http://www.gromacs.org/search before posting! Please don't
post (un)subscribe requests to the list. Use the www interface or
send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>. Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
-- gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the
archive at http://www.gromacs.org/search before posting! Please don't
post (un)subscribe requests to the list. Use the www interface or send
it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>. Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
-- ========================================
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
======================================== -- gmx-users mailing list
gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to gmx-users-requ...@gromacs.org. Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
-- ========================================
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
======================================== -- gmx-users mailing list
gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to gmx-users-requ...@gromacs.org. Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
