Re: [AMBER] DOPC lipid bilayer deformation in Implicit MD simulation using Lipid14 force field in Amber18

From: Gould, Ian R <i.gould.imperial.ac.uk>
Date: Tue, 7 Jan 2020 08:37:25 +0000

Lipid 14 was not parameterized for implicit solvent simulations we only recommend that it be used with explicit water.

"Education: that which reveals to the wise, and conceals from the stupid, the vast limits of their knowledge."
Mark Twain

 
Professor Ian R Gould, FRSC.
Professor of Computational Chemical Biology
 
Department of Chemistry
Imperial College London
Exhibition Road
London
SW7 2AY
 
MSRH
Imperial College White City Campus
80 Wood Lane
London W12 0BZ
 


´╗┐On 07/01/2020, 07:20, "Bhat Zahoor" <dr.zahoor11.gmail.com> wrote:

    
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    Hello,
    
    I have been trying to simulate DOPC lipid bilayer model in implicit solvent
    using Lipid14 force field in Amber18 but after a few ns of production run,
    the lipid bilayer starts to deform and behave more like a liposome.
    I have prepared the bilayer model using Charmm-Gui web interface and then
    minimized the model using Amber18. While simulating the same system in
    explicit solvent and same force field for 100 ns did not show membrane
    deformation. I just want to know, whether there is any error or this is
    normal for a bilayer simulation in Implicit solvent.
    
    *Zahoor Ahmad Bhat*
    Research Scholar
    Multidisciplinary Centre for Advanced Research and Studies
    Jamia Millia Islamia
    New Delhi - 110025
    India
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Received on Tue Jan 07 2020 - 01:00:02 PST
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