[gmx-users] Membrane: anisotropic pressure coupling
Rebeca García Fandiño
regafan at hotmail.com
Wed Jul 23 19:44:21 CEST 2008
I am new in Gromacs, and I am trying to simulate the interaction between a DOPC membrane and a protein.
I have equilibrated my system at constant volume and now I would like to switch to constant pressure.
I think the best option for me is to use ANISOTROPIC pressure, because I want to study the ondulations produced in the membrane due to the protein. Do you recommend anisotropic pressure for this? or semiisotropic would be enough?
Another question is about the values of tau_p and ref_p. I have read in the manual that in the case of anisotropic pressure I should use 6 values. Which values do you recommend to use? Should I use also 6 values for compressibility and ref_p? Pcoupl = BerendsenPcoupltype = anisotropictau_p = 2.0 2.0 2.0 2.0 2.0 2.0 compressibility = 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5ref_p = 1.0 1.0 1.0 1.0 1.0 1.0 Thank you very much for your help in advance. Best wishes, Rebeca García FandiñoParc Cientific de Barcelonaregafan at hotmail.com
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