Hello Ross,
Thanks for the reply. My mistake I mean lipid11. I was using lipid11 for
POPC, POPE and cholesterol. I think you are making a very good point. For
the membrane-protein system, I probably should try a simply lipid layer,
such as POPC alone. I am currently running Amber12 and using the lipid11.
Is the revision on surface tension incorporated in this version?
Thanks again.
Victor
On Wed, May 27, 2015 at 8:43 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Victor,
>
> I do not understand what you mean by Amber FF? - There is no such thing as
> the "AMBER Force Field". If you are using Lipid 11 for the lipids then you
> need a constant surface tension term. This would explain why your area per
> lipid is dropping so much. Ideally you should be using Lipid 14 for the
> lipids which does not require constant surface tension but we have not yet
> publicly released Cholesterol parameters for Lipid 14. We are waiting for
> the manuscript to be accepted before we make these available. Using Lipid
> 11 Cholesterol parameters with Lipid 14 leads to incorrect lipid membrane
> densities - we tested this extensively as part of our parameterization for
> Lipid 14.
>
> As such it is not clear what you are actually doing here. Lipid membrane
> simulations are notoriously complicated and fickle - temperature is
> critical. With regards to the tutorial - that is, I expect, a much smaller
> system than your are trying to simulate, it also did not include a mixture
> of lipids or cholesterol. Your system is WAY more complicated and one could
> expect the equilibration procedure to be significantly more involved.
>
> All the best
> Ross
>
> > On May 27, 2015, at 8:35 AM, Victor Ma <victordsmagift.gmail.com> wrote:
> >
> > Hello Ross,
> >
> > Thanks for the kind reply. I am using Amber FF (2:2:1
> > POPC:POPE:Cholesterol). I am using 303 K because I am using the same
> lipid
> > combination as the tutorial. I do not know the experimental area per
> lipid
> > for my system, which is GPCR. Does it depend on the biological system or
> > the lipid combination I use in the simulation?
> >
> > I agree that 14ns is a little short for convergence. But in the tutorial,
> > the simulation converged after only 20ns. So I thought I should be
> getting
> > close.
> >
> > Thank you!
> >
> > Victor
> >
> >
> > On Tue, May 26, 2015 at 6:16 PM, Ross Walker <ross.rosswalker.co.uk>
> wrote:
> >
> >> Hi Victor,
> >>
> >> Do you know what the experimental area per lipid is? - This will give
> you
> >> an idea if you are close or not. Typically the box sizes produced by the
> >> charmm lipid builder are too large so you get a massive decrease in box
> >> size as you simulate. This is especially true when packed around a
> protein.
> >> Also what lipids are these and with what force field? - Is 303K
> appropriate
> >> for the lipid you are simulating? You should check what the experimental
> >> transition temperature is and make sure you are above the transition for
> >> gel phase.
> >>
> >> The lipids moving in and out is likely just imaging artefacts.
> >>
> >> What's the scale on your x axis? Frames???, ns?, picoseconds? - It's
> hard
> >> to comment on convergence rate with units. If I assume frames then 1400
> >> frames is 14ns assuming 10ps per frame based on your input below. 14ns
> is
> >> way too short to see convergence of the area per lipid. Something in the
> >> region of 100ns+ is likely needed.
> >>
> >> All the best
> >> Ross
> >>
> >>> On May 26, 2015, at 2:13 PM, Victor Ma <victordsmagift.gmail.com>
> wrote:
> >>>
> >>> hello Amber community,
> >>>
> >>> I am following the Amber Tutorial 16 on running lipid simulation and I
> am
> >>> in the equilibration stage with no restrains at all. Here is my input
> >> file:
> >>> &cntrl
> >>> imin=0,
> >>> ntx=5,
> >>> irest=1,
> >>> ntc=2,
> >>> ntf=2,
> >>> tol=0.0000001,
> >>> nstlim=2500000,
> >>> ntt=3,
> >>> gamma_ln=1.0,
> >>> temp0=303.0,
> >>> ntpr=5000,
> >>> ntwr=5000,
> >>> ntwx=5000,
> >>> dt=0.002,
> >>> ig=-1,
> >>> ntb=2,
> >>> ntp=2,
> >>> cut=10.0,
> >>> ioutfm=1,
> >>> ntxo=2,
> >>> /
> >>> /
> >>>
> >>> I am checking the output trajectory in VMD and I am not quite sure
> >> whether
> >>> the lipids look all right. They are kind of loose especially the ones
> on
> >>> the edge. When I visualize them dynamically, it feels like a few of
> them
> >> on
> >>> the boundary are "appearing" and "disappearing". I suppose that's the
> >>> periodic boundary box? The trajectory has been re-imaged using all the
> >>> protein residues as centre. Also I calculated the "lipids per area" and
> >>> clearly they are not converged yet. But I am a bit surprised. Because
> in
> >>> the tutorial, lipids seem to have converged rather fast at the
> beginning
> >> of
> >>> the simulation.
> >>>
> >>> I attached some pictures and look forward to any comments!
> >>>
> >>> Thank you!!
> >>>
> >>> Victor
> >>>
> >>
> <printme.png><vmdscene.jpeg><vmdscene_1.jpeg>_______________________________________________
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Received on Wed May 27 2015 - 10:00:02 PDT
