[gmx-users] Re: Simulating a semi-membrane protein

[Catarina Santos]

Dear Pavithrakb,

First of all, your choice will depend on the available parameters for the
lipid molecules that you want to simulate (check the Lipidbook
repository<http://lipidbook.bioch.ox.ac.uk/>
).

Concerning the GROMOS force fields the most recent lipid parameters are the
ones included in the G54A8 force field (Reif_2012_JCTC_8_3705,
Reif_2013_JCTC_9_1247).

However, Poger et al proposed an add-on to the standard G53A6
(Poger_2010_JCC_31_1117
and Poger_2010_JCTC_6_325), lately incorporated in the G54A7
(Schmidt_2011_EBJ_40_843), that is commonly used and yields good results
for the analysed lipid parameters (i.e. in agreement with experimental
measurements).

Despite the aforementioned papers, you might want to go through the
references listed bellow concerning several lipid parameters for GROMOS
force fields or proposed modifications (e.g. cutoff schemes, charges,
charge group distributions):

- Berger lipids: Berger_1997_JB_72_2010
- Ash lipids: Tieleman_2006_JPCM_18_S1221
- G43A1-S3: Chiu_2009_JPCB_113_2748
- G45A3: Schuler_2001_JCC_22_1205, Chandrasekhar_2003_EBJ_32_67
- Modified Berger: Anezo_2003_JPCB_107_9424
- Modified ffG45A3: Anezo_2003_JPCB_107_9424
- Kukol lipids: Kukol_2009_JCTC_5_615
- G53A6L: Poger_2010_JCC_31_1117, Poger_2010_JCTC_6_325
- G54A7: Schmidt_2011_EBJ_40_843
- G54A8: Reif_2012_JCTC_8_3705, Reif_2013_JCTC_9_1247

-- 

Catarina Santos
Research Student
Molecular Simulation Group
Instituto de Tecnologia Química e Biológica
Universidade Nova de Lisboa
Av.da República, Apartado 127
2781-901 Oeiras, Portugal