Re: [AMBER] GAFFlipid parameters

From: Benjamin D Madej <>
Date: Wed, 4 Jun 2014 21:13:51 +0000

Hi Aldo,

It is fairly common to transfer force fields between MD simulation programs. It is likely that they would like to compare force fields within the same MD program. There are indeed several lipid force fields available for Gromacs with different parameterization schemes and levels of detail (coarse-grain, united-atom, all-atom).

It is certainly possible to run Lipid14 in Gromacs. I have not done it myself but I know there are people out there that have done it. See:

I would recommend running the Lipid14 force field with Amber 14. One important reason is because of the significant performance gains from the GPU accelerated pmemd.cuda code. It is now fairly routine to run several hundred ns of lipid bilayer MD with Amber. Amber also is also expanding its tools to build and analyze these lipid simulations. For example, it is fairly straightforward to convert a CHARMM lipid structure to run in Amber with the Lipid14 force field. Cpptraj also now includes lipid analysis functions.

All the best,
Ben Madej
UCSD Chemistry and Biochemistry

From: Aldo Segura []
Sent: Wednesday, June 04, 2014 5:56 AM
To: AMBER Mailing List
Subject: Re: [AMBER] GAFFlipid parameters


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
     AMBER mailing list



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Received on Wed Jun 04 2014 - 14:30:02 PDT
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