[gmx-users] Naughty Vacuum Bubble in our Vesicle!
rajat desikan
rajatdesikan at gmail.com
Mon Oct 27 17:32:36 CET 2014
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 warming the waters
slowly with an SA protocol while restraining the lipids.
Regards,
On Monday, October 27, 2014, André Farias de Moura <moura at ufscar.br> wrote:
> 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, pressure
> coupling with ordinary pressure values cannot fix a vacuum bubble just like
> it would for an isotropic liquid, because the elimination of the bubble
> would then require that both lipid packing and interface curvature should
> change (your result clearly says that it is preferable to form a vacuum
> bubble than to shrink the vesicle itself - and this is not a simulation
> issue neither it is an artifact, this is just a balance between different
> surface energy contributions arising from the vacuum cavity and the vesicle
> interfaces). As I see it, you should try to remove fewer water molecules
> from the original cavity (maybe relaxing the distance criteria to remove an
> overlapping water molecule).
>
> I hope it helps.
>
> best,
>
> Andre
>
>
> On Mon, Oct 27, 2014 at 1:15 PM, Björn Sommer <bjoern at cellmicrocosmos.org
> <javascript:;>>
> wrote:
>
> > 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 genbox. The
> > membrane-intersecting water was removed by a custom Python script in VMD.
> > After the removel or the intersecting water, the water seems to be very
> > well enclosed in the inner membrane, without intersecting water atoms and
> > with only a little space between the inner head groups and the water.
> >
> > The system minimization in water (spc216) worked pretty well, but after
> > NPT-equillibration I found a vacuum bubble in the intracellular room of
> the
> > vesicle.
> >
> > I tried to do a NVT-equillibration before the NPT, which ended with the
> > same result.
> >
> > Using different barostats (parrinello-rahman, Berendsen) and
> > refcoord-scaling options could'nt change anything, too.
> >
> > To "repair" the vacuum I tried to manually insert some water using pymol,
> > after equillibrating this system again, i got the same result with an
> even
> > bigger bubble in the centre.
> >
> > Analysing my system with g_energy showed a volume increase about 400nm³,
> > which is rawly 4% more than the volume of the starting system. The
> systems
> > energy increased by 20 kJ/mol.
> >
> > Trying to simulate the vesicle with the vacuum bubble inside resulted in
> a
> > deformed vesicle and an increased distance between the outer and the
> inner
> > lipid layer.
> >
> > The NPT.mdp file I used is the following:
> >
> > ;**********************************************************
> > ; NEIGHBORSEARCHING PARAMETERS =
> > ; nblist update frequency =
> > nstlist = 5
> > ; ns algorithm (simple or grid) =
> > ns_type = grid
> > ; Periodic boundary conditions: xyz or none =
> > pbc = xyz
> > ; nblist cut-off =
> > rlist = 1.6
> >
> > ; OPTIONS FOR ELECTROSTATICS AND VDW =
> > ; Method for doing electrostatics =
> > coulombtype = PME
> > rcoulomb_switch = 0.0
> > rcoulomb = 1.6
> > ; Method for doing Van der Waals =
> > vdw_type = Shift
> > ; cut-off lengths =
> > rvdw_switch = 0.9
> > rvdw = 1.0
> > ; Apply long range dispersion corrections for Energy and Pressure =
> > DispCorr = AllEnerPres
> >
> > ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
> > ; Temperature coupling =
> > tcoupl = Berendsen
> > ; Groups to couple separately =
> > ;TODO: für mehrere Lipidtypen anpassen
> > tc-grps = CHO DPC DPE SOL
> > ; Time constant (ps) and reference temperature (K) =
> > ;TAUT
> > tau_t = 0.1 0.1 0.1 0.1
> > ;REFT
> > ref_t = 300 300 300 300
> > ; Pressure coupling =
> > Pcoupl = berendsen
> > Pcoupltype = isotropic ;semiisotropic
> > ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
> > tau_p = 4.0 4.0
> > compressibility = 3e-5 3e-5
> > ref_p = 1.0 1.0
> > refcoord-scaling = no
> >
> > ; GENERATE VELOCITIES FOR STARTUP RUN =
> > gen_vel = no
> > gen_temp = 105
> > gen_seed = 473529
> >
> > ; OPTIONS FOR BONDS =
> > constraints = all-bonds
> > fourierspacing =
> > pme_order = 6
> > optimize_fft = yes
> > ; Type of constraint algorithm =
> > constraint_algorithm = Lincs
> > ; Do not constrain the start configuration =
> > unconstrained_start = no
> > ; Highest order in the expansion of the constraint coupling matrix =
> > lincs_order = 4
> > ; Lincs will write a warning to the stderr if in one step a bond =
> > ; rotates over more degrees than =
> > lincs_warnangle = 30
> >
> > ;**********************************************************
> >
> > Also, I tried to relax my vesicle under NPT in vacuum in order to add
> > water in a later step, but the NPT ended with a lot of LINCS warning
> > (rotation more than 30 degrees). Okay, we read already that there are
> some
> > information in the gmx-list discussing this problem, but the question is
> if
> > it basically makes sense to follow the idea of a vaccum simulation or if
> we
> > should directly start with solvated system in any case.
> >
> > Can you suggest us any method to solve this problem or maybe help us to
> > improve our .mdp? Would be great!
> >
> > Best wishes,
> > Manuel (and Björn)
> >
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>
>
> --
> _____________
>
> Prof. Dr. André Farias de Moura
> Department of Chemistry
> Federal University of São Carlos
> São Carlos - Brazil
> phone: +55-16-3351-8090
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--
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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