regarding your first question, the definition of gamma is not correct, you are getting energy/length⁴ instead of energy/area (multiply by Lz instead of dividing by it)
2011/3/9 Pedro Alexandre de Araújo Gomes Lapido Loureiro <[email protected]>: > Hi, > >> 1- g_energy is giving #Surf*SurfTen by default. On the other hand surface >> tension can be obtained by gamma = (Pzz - (Pxx+Pyy)/2) / Lz. i.e >> Pres-XX-(bar), Pres-YY(bar), Pres--(bar) >> >> Can anyone tell me what the difference between these two is? > > They should be equal, bearing in mind units conversion. > >> >> 2- In pressure coupling settings there is surface_tension option which I >> guess is applicable where surface tension needs to be kept fixed. If one >> want to calculate surface tension I dont think this option make sense. Am I >> right? > > Yes. >> >> 3- I am using the following setting: I calculate the average for a 2ns run >> and different start times as shown below. Although T, P and other quantities >> are equilibrated after 200ps, surface tension is not giving a constant >> value. Is that because I am not using berenden P coupling? (As mentioned in >> the manual surface tension works with berendsen) >> >> Pcoupl = Parrinello-Rahman >> Pcoupltype = isotropic >> tau_p = 1 1 >> compressibility = 4.5e-5 >> ref_p = 40 >> >> >> time period for which average is calculated Average RMSD >> Fluct. Drift Tot-Drift >> >> ------------------------------------------------------------------------------- >> 1-2000 ps run: #Surf*SurfTen 6.43844 3588.74 >> 3588.35 0.091406 182.721 >> 500-2000 ps #Surf*SurfTen 12.8518 3605.72 >> 3605.26 0.132126 198.189 >> 1000-2000ps #Surf*SurfTen 18.8821 3610.97 >> 3610.8 0.11819 118.191 >> 1500-2000ps #Surf*SurfTen 23.0072 3585.51 >> 3584.93 -0.444037 -222.019 >> > This question is anything but trivial! Look at the RMSD values compared with > the averages. The dispersion is so high that you can't be sure if this is or > not equilibrated. > > >> >> 4- Assuming I am getting surface tension for a cubic box, to compare this >> with reported values in literature I need to divide by 6 (no. of surfaces)? > > No. You have to divide by the number of interfaces (2 for a bilayer immersed > in water, for instance) > > >> >> 5- Does box six affect the results? (mine is 3.3 nm ). >> > Yes, but see answer 3, above. > >> >> Thank you, >> >> >> >> >> >> >> >> >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
