Re: [AMBER] membrane protein simulation

From: Ross Walker <>
Date: Tue, 26 May 2015 18:16:22 -0700

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

> On May 26, 2015, at 2:13 PM, Victor Ma <> 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 Tue May 26 2015 - 18:30:02 PDT
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