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
> >
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Received on Wed May 27 2015 - 09:00:02 PDT
