Re: [gmx-users] Anisotropic Pressure

[Matteo Guglielmi]

Berk Hess wrote: From: Matteo Guglielmi <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org> To: GMX-LIST <gmx-users@gromacs.org> Subject: [gmx-users] Anisotropic Pressure Date: Fri, 15 Jun 2007 19:11:50 +0200 Hello Folks, Is there any difference between these two anisotropic pressure setup? ### 1st setup ### pcoupl                   = berendsen pcoupltype               = anisotropic tau_p                    = 5.0      5.0      5.0      0.0    0.0    0.0 compressibility          = 4.53e-5  4.53e-5  4.53e-5  0.0    0.0    0.0 ref_p                    = 1.025    1.025    1.025    0.0    0.0    0.0 ### 2nd setup ### pcoupl                   = berendsen pcoupltype               = anisotropic tau_p                    = 5.0      5.0      5.0      5.0    5.0    5.0 compressibility          = 4.53e-5  4.53e-5  4.53e-5  0.0      0.0      0.0 ref_p                    = 1.025    1.025    1.025    1.025  1.025  1.025 If the compressibility is zero, the corresponding unit-cell degree of freedom will not change, so effectively there is no difference. Which one would you suggest for anisotropic coupling (solvated pore immersed into a membrane) Neither, you should probably use surface-tension coupling. Berk. Ok, thanks for the answer. Actually I never used surface-tension coupling but the manual says: "Surface tension coupling for surfaces parallel to the xy-plane." ... which is my case. "Uses normal pressure coupling for the z-direction, while the surface tension is coupled to the x/y dimensions of the box." Ok. "The first ref_p value is the reference surface tension times the number of surfaces [bar nm]," I have a lipid bilayer membrane su I guess I should multiply by 2 the surface tension value for which I do not have any guess about its value. "the second value is the reference z-pressure [bar]." Ok... I could use the default value (phosphatidylethanolamine membrane in water). "The two compressibility [bar−1] values are the compressibility in the x/y and z direction respectively." What about the first one? For the z direction I could use the water compressibility... "The value for the z-compressibility should be reasonably accurate since it influences the convergence of the surface-tension, it can also be set to zero to have a box with constant height." Any suggestion on how I could complete the surface tension coupling set up? MG.

_______________________________________________
gmx-users mailing list    gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php