normal md parameters

  • Norbert
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8 years 10 months ago #845 by Norbert
md parameters was created by Norbert

Using MARTINI, I would like to study the association of two transmembrane peptides in a membrane environment.
So, I am currently trying to create a pre-equilibrated DOPC bilayer consisting of 418 DOPC and 5000 CG water molecules. For this I am using the bilayer self-assembly tutorial with the following parameters:

tcoupl berendsen
tc-grps DOPC W
tau_t 1.0 1.0
ref_t 300 300

Pcoupl berensen
Pcoupltype isotropic
tau_p 0.5
compressibility 5e-5
ref_p 1.0

I do not obtain a bilayer on a 1 micro second time scale.

Please could you help me?
Thank you very much


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8 years 10 months ago #846 by djurre
Replied by djurre on topic md parameters
Your mdp options seem fine. It is possible that instead of a bilayer another stable structure (different phase) forms. If you would restart the simulations, with different starting velocities, a bilayer would probably form.

However, probably the easier solution would be to use the pre-equilibrated membrane you can find on the website (Downloads > Example applications > DOPC and POPE membranes). The patch is smaller, but you could easily multiply it (eg using genconf in gromacs).

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