I want to create MGDG (monogalactosyldiacylglycerol) reversed hexagonal phase, but I have a problem. I constructed a system that consists of two bilayers and an inner water layer between these two bilayers and the outer water layer. I used the OPLS-AA force field. I have a problem, my system looks like in these image in 300 ns in the attachment. My lipids don't want to create the hexagonal phase. I just have clusters of water and places in which lipids from opposite bilayers are close to each other, but they don't want to turn and change their position and create a reversed hexagonal phase. I get a piece of advice that probably my lipid head groups (my head group consists of galactose) interacts too much with each other, so I want to change my non-bonded params and change Lennard-Jones interactions http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf
I heard that I should check the density of galactose or temperature of crystallization of galactose, do you know how to do that? So I must check experimental value and create a system that consists of only galactose and check density in proper temperature and compare to that in experimental value, but how to do that? Find experimental value is an easy task. Then I would create a system consists of only galactose and check the density at the same temperature as in experimental value, then if it is the difference I must change something but how??? Which things and which value I should put???
For example I have something like that
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 3 Yes 0.5 0.5
;
[ atomtypes ]
;
C 12.0110 0.000 A 3.75000e-01 4.39320e-01 ; ORIG sp2 pep.bond./carbonyl
So I will change in atomtypes these values????:
3.75000e-01 4.39320e-01
but in which values, I should change these values maybe I should get these values from different force field??????
Do you know any tutorials/books which could help me?
- Badges
- Science topic
- Similar topics
- Gels