Dear Andre, Rajat, Stephane, Patrick Justin, Dear Vesicle Simulators!
Thank your for all your clues, we really appreciate them and they helped
us to solve our problem!
Some weeks ago, I asked you about my problem while simulating a vesicle
using united-atoms method (ffG45a3).
The main
Hi Björn,
my five cents. Did you consider constructing the system using MARTINI,
equilibrating it with artificial pores and then back-map it to all-atom?
Otherwise, I guess this artificial pore strategy could be applied to an
all-atom system, but it'd be way more lengthy.
Ciao,
Patrick
Le
Dear Manuel/Björn,
I think Patrick has a point, an artificial pore should allow the solvent to
equilibrate itself across the bilayer, but you need to choose atomistic and
coarse grained force fields that yield very close areas per lipid (for
planar bilayers, for instance), otherwise the atomistic
Dear Rajat,
Dear Andre,
Dear all,
thanks again for your help.
1) I'm simulating an united atoms model and isotropic pressure is used,
not coarse-grained (this would be indeed more simple, because faster and
much more examples are available).
2) Yes, I added additional water bubbles of
On 10/28/14 6:23 AM, Björn Sommer wrote:
Dear Rajat,
Dear Andre,
Dear all,
thanks again for your help.
1) I'm simulating an united atoms model and isotropic pressure is used, not
coarse-grained (this would be indeed more simple, because faster and much more
examples are available).
2) Yes, I
Dear all,
we are trying to simulate a vesicle in water using united-atoms
(Gromos96/ffG45a3). The system was modelled with the VesicleBuilder and
the MembraneEditor. So first the vesicle was built (with 3 components: 2
PC, 1 Chol), and then it was embedded in a water (spc216) box with
Dear Manuel/Björn,
you cannot ignore that vesicle-like structures have a complex interfacial
energy, with terms arising from both the packing of lipids and the
curvature of the interface, among other factors. If it happens that you
placed the wrong number of water molecules inside the cavity,
Hi Bjorn,
I agree with Andre. Pack more water molecules inside the vesicle than what
you currently have. It is likely that the water penetrates quite a bit into
the headgroups, and hence you need more waters than you think (since water
can hydrogen bond with the lipid head groups). Also try
Hello Bjorn
I don't know if it related to your problem, but I see a typo in our mdp file
for the pressure coupling:
Pcoupltype = isotropic ;semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p= 4.0 4.0
compressibility
Dear Andre, Rajat Stephane,
thanks a lot for your light-speed suggestions!
@More Water Idea
I'll try to remove as less water as possible in my next try.
But, what bothers me is the fact, that I manually added some water after
the vacuum bubble was formed and equillibrated again, which
Dear Bjorn,
A few thoughts:
1) Are you simulating a coarse grained system (Martini) or an all-atom
system. Isotropic pressure coupling may be more appropriate for a vesicle
because of its spherical symmetry.
2) When you manually added water, did you do it in the vacuum bubble region
only?
3) What
Dear Manuel/Björn,
based on your description, I guess that placing some more water after the
bubble has formed may not work as expected, because the bilayer forming the
vesicle might be somehow strained, that's why a suggested stepping back to
the system before equilibration. I think the number
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