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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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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Received on Wed Jun 04 2014 - 06:00:07 PDT
