Re: [AMBER] membrane protein simulation

From: Ross Walker <>
Date: Wed, 27 May 2015 08:43:34 -0700

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

> On May 27, 2015, at 8:35 AM, Victor Ma <> 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 <> 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 <> 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>_______________________________________________
>>> AMBER mailing list
>> _______________________________________________
>> AMBER mailing list
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Wed May 27 2015 - 09:00:03 PDT
Custom Search