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:
http://ambermd.org/#ff
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
SDSC
________________________________________
From: Aldo Segura [asegurac666.yahoo.com.mx]
Sent: Wednesday, June 04, 2014 5:56 AM
To: AMBER Mailing List
Subject: Re: [AMBER] GAFFlipid parameters
Hi,
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.
Best,
Aldo
=======================================
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 <aaju.yandex.ru> 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" <callum.dickson09.imperial.ac.uk>:
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.
Cheers,
Callum
________________________________________
From: [1]amber-bounces.ambermd.org [[2]amber-bounces.ambermd.org] on
behalf of ц║ц▌ц■ц┴ц░ц┴ц▌ц│ ц║ц▄ц┘ц▀ц⌠ц│ц▌ц└ц▓ц│ [[3]aaju.yandex.ru]
Sent: 04 June 2014 10:01
To: [4]amber.ambermd.org
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]
http://lipidbook.bioch.ox.ac.uk/ , but unfortunately this file
does
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
are
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.
[6]aaju.yandex.ru
References
1. [7]
http://lipidbook.bioch.ox.ac.uk/
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[9]
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[11]
http://lists.ambermd.org/mailman/listinfo/amber
References
1. mailto:amber-bounces.ambermd.org
2. mailto:amber-bounces.ambermd.org
3. mailto:
aaju.yandex.ru
4. mailto:amber.ambermd.org
5.
http://lipidbook.bioch.ox.ac.uk/
6. mailto:aaju.yandex.ru
7.
http://lipidbook.bioch.ox.ac.uk/
8. mailto:AMBER.ambermd.org
9.
http://lists.ambermd.org/mailman/listinfo/amber
10. mailto:AMBER.ambermd.org
11.
http://lists.ambermd.org/mailman/listinfo/amber
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AMBER mailing list
AMBER.ambermd.org
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Received on Wed Jun 04 2014 - 14:30:02 PDT
