normal 512 DPPG bilayer

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13 years 3 months ago #453 by nanogod
512 DPPG bilayer was created by nanogod
Hi,
I am currently trying to selfassemble a 512 lipid bilayer consisting of DPPG lipids I made by combining the head group of a DOPG and the tail of a DPPC lipid. However, I have two problems.

Firstly, I made the 512 lipid bilayer by expanding a 128 bilayer in the x and y direction. The 128 bilayer is fine, but my 512 bilayer starts to move up and down (it makes a wave like motion) and single lipids almoste moves out of the bilayer. I dont know if this is normal for a 512 bilayer as I have ever only worked with 128 bilayers.

Secondly, polarized water moves across the bilayer. I know the polarized water have been parameterized so that this mimic all atom simulations better, but in my case it seems to occur abit too much.


I have to speculations about why this happens:

I was reading the article "Polarizable Water Model for Coarse-Grained MARTINI Force Field" and was unsure if the following parameters from the martini_v2.P.itp was used in the MD simulation or only in the minimization step:

;[bonds]
; i j funct length force const.
1 2 1 0.14 50000
1 3 1 0.14 50000

or if it was disabled as by default with ; infront of it?

In my MD simulation this setting is disabled but might this be the reason why water moves across the membrane and hence makes it unstable and then starts to make a wave motion?

Another speculation of mine is that the expansion of the 128 lipid bilayer isnt stable enought and that I shall have to make a selfassemble of a 512 bilayer from the start rather than using the -nbox function?

Hope you can help even though my explanation might be abit messy :)

/Morten

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13 years 3 months ago #454 by siewert
Replied by siewert on topic 512 DPPG bilayer
The use of bonds is only required during minimization; for production runs you should have the constraints (so the bonds section should be commented out using';')

Are you sure you use the mdp options appropriate for the polarizable water model? You should have a dielectric screening set to 2.5 rather than 15. See martini_v2.P_example.mdp

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