Re: [AMBER] GAFFlipid parameters

From: Aldo Segura <>
Date: Wed, 4 Jun 2014 05:56:48 -0700 (PDT)


Is there any particular reason for use GAFF lipid force field in Gromacs?

MD simulation of membrane systems is not a trivial task, but I think there are several examples and papers using Gromacs for such systems.

You should ask in Gromacs mailing list also.



Aldo Segura-Cabrera
Postdoctoral Fellow
Division of Experimental Hematology and Cancer Biology
Cancer and Blood Diseases Institute
Cincinnati Children's Hospital Medical Center
3333 Burnet Ave, MLC 7013, Cincinnati OH 45229


El Miércoles, 4 de junio, 2014 8:27:23, Антипина Александра <> escribió:

  Dear Callum,

  thanks for your quick reply!

  As  far as I know Lipid14 parameters are not correct to reproduce some
  parameters as,for example, volume per lipid. While GAFFlipid force field is
  good for calculation of volume and other parameters. So I think GAFFlipid
  force field 2012 is more suitable for use at the present time.

  I ask you to correct me if I'm wrong.

  Alexandra Antipina

  04.06.2014, 15:42, "Dickson, Callum J" <>:

    Hi Alexandra,
    I would suggest you use the updated Lipid14 parameters for POPC - these
    use (and have been tested with) the correct phosphorus angle parameters
    from gaff.dat.
    From: [1] [[2]] on
    behalf of ц║ц▌ц■ц┴ц░ц┴ц▌ц│ ц║ц▄ц┘ц▀ц⌠ц│ц▌ц└ц▓ц│ [[3]]
    Sent: 04 June 2014 10:01
    To: [4]
    Subject: [AMBER] GAFFlipid parameters
    Dear Amber Developers!
    I am working on MD simulations of POPC lipids. I would like to employ the
    GAFFlipid force field for simulations of POPC lipids with the use of the
    Gromacs package. I found the file with the force field parameters on the
    site [1][5] , but unfortunately this file
    not contain all parameters needed, and as far as I understood it serves as
    an additional file for the Amber package, so that the rest of parameters
    included in file gaff.dat of the Amber package. But as far as I know gaff
    parameters are constantly changing, for example, the parameters of P
    (phosphorus) for calculating the bond angle force constant. As I am not a
    user of the Amber package, it is difficult for me to identify which
    parameters were used for the development of your GAFFlipid force field in
    2012. I would be grateful if you helped me to obtain all the parameters of
    GAFFLipid force field for a POPC molecule.
    Alexandra Antipina
    Postgraduate student of Saint-Petersburg State University, Russia.
    1. [7]
    AMBER mailing list
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Received on Wed Jun 04 2014 - 06:00:07 PDT
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