Lets make it clear. I can not tell you if the atoms in the second
frame are in the
box or not! You have to visualize it!
Honestly it is not in the first frame I can not see how it would in
the second!
You have to build a reference structure that has the bilayer in one
piece, then
the nojump option can actually to the job you want.
On Nov 6, 2009, at 10:37 AM, maria goranovic wrote:
So lets say that I delete the first frame from the trajectory in
which some atoms might have been outside the box. Everything should
be within the box once the simulation starts (from the second frame
onwards)? So the procedure should work if the reference structure is
the second frame? I have tried that, and it fails as well.
On Thu, Nov 5, 2009 at 4:40 PM, XAvier Periole <x.peri...@rug.nl>
wrote:
The nojump option will not apply the pbc when an atom is crossing the
box boundaries ... in your case your bilayer should definitely be in
the
center of your box and all the atoms in !!!! If not ot course it
does not work!
On Nov 5, 2009, at 4:33 PM, maria goranovic wrote:
my starting structure looks quite all right to me. everything is in
the box (except the tails of some lipids) .. wonder whats wrong.
thank you verymuch for helping
On Thu, Nov 5, 2009 at 4:04 PM, XAvier Periole <x.peri...@rug.nl>
wrote:
On Nov 5, 2009, at 4:00 PM, maria goranovic wrote:
Hi Xavier,
Thanks for the clear instructions. The bilayer is not in one piece
in the z direction after the -pbc nojump for some reason.
the problem might be from your starting structure, everything
should be in the box!
Or you may be facing strange/funny/incomprehensible behavior ...
after the third step, the water is in the right place, but the
bilayer has expanded to periodic boxes in the xy plane. so the
center of mass of the lipid molecules is not really being centered
in the box ?
On Thu, Nov 5, 2009 at 3:34 PM, XAvier Periole <x.peri...@rug.nl>
wrote:
you need to do:
1- trjconv -pbc nojump; this keeps your bilayer in one piece on
the z direction
2- trjconv -center; using the bilayer to center and the system as
output; this will
translate your bilayer on the z axis and normally not modify it on
the xy plan.
3- trjconv -pbc mol; will put your lipids in one piece in the box;
I believe this
step cn be coupled to the previous quite safely.
On Nov 5, 2009, at 3:23 PM, maria goranovic wrote:
One more note about -pbc nojump. I typically use -pbc mol. Using
pbc nojump succeeds in keeping the center of the bilayer at 0 0
0, but the atoms have moved way out of the simulation box
resulting in a dilute system
On Thu, Nov 5, 2009 at 2:31 PM, maria goranovic <mariagorano...@gmail.com
> wrote:
Centering on one atom has a problem that the lipid diffuses in
the plane of the membrane, and as a result, the entire system
starts to center around the lipid resulting in a simulation box
which translates a lot in the bilayer plane.
The splitting is not a problem, yes. But during the simulation
period when the bilayer is not split, it diffuses quite a bit
along the bilayer normal (after use of -pbc mol, and centering
around the lipid center of mass). a plot of the lipid center of
mass shows the bilayer diffusing along z, when its not split.
On Thu, Nov 5, 2009 at 2:25 PM, XAvier Periole <x.peri...@rug.nl>
wrote:
On Nov 5, 2009, at 2:02 PM, Justin A. Lemkul wrote:
maria goranovic wrote:
I did use -pbc nojump, but that does not help
What about entering on a central lipid tail atom, I suggested
some time ago? The bilayer probably just splits across periodic
boundaries, so this is not really a problem; just a visualization
artefact.
The splitting is not a problem and I think that centering using
one lipid (tail) won't change the problem if
the bilayer is cut half! Or the -pbc mol should be applied ...
-Justin
The drift is about 1 nm per 10 microseconds .
(this is a martini simulation)
On Thu, Nov 5, 2009 at 1:02 PM, XAvier Periole <x.peri...@rug.nl <mailto:x.peri...@rug.nl
>> wrote:
On Nov 5, 2009, at 12:09 PM, maria goranovic wrote:
Hello All (and especially Berk)
This is an update of the problem that I was facing earlier. I
used to tau_p of 3.0 ps, and the problem does not go away,
the
bilayers still drifts in the simulation box. So this is
probably a bug then?
How much is the drift (nm/ns)? Did you use removal of center of
mass
of the entire system of
bilayer/solvent separately?
I still cannot understand how to put the bilayer back into
the
center of the simulation box. As suggested by Justin, I
tried to
use just one tail atom of a lipid for centering, but that did
not work either.
I noticed that my bilayer, which is initially at the center
of
the simulation box, separates into two leaflets at the box
edges
from the very first step of the simulation itself, but i am
not
able to correct that using the -center and -boxcenter zero
options. Can someone please make a suggestion and help?
You have to do use -pbc nojump first and then center ...
Thank you so much
-Maria
-- Maria G.
Technical University of Denmark
Copenhagen
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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