> > Dear users > I was tyring to run an npt simulation of membrane. My mdp is:
> As advised in a recent workshop on http://www.csc.fi/chem/course/gmx2007/ > i am using Parrinello-Rahman instead of berendsen. The problem is that the > box size is getting reduced to 9.99448 9.99448 9.25077 from 10.0 10.0 10.0 > and water is compressing the bilayer. This is the purpose of equilibration with NPT - to fix density issues. The contraction in Z suggests that your membrane is insufficiently dense in that direction, or has some vacuum pockets. That's not a problem in itself so long as you equilibrate long enough. Berendsen P-coupling will likely do the same thing. > I also tried anisotropic coupling > pcoupltype = anisotropic > tc-grps = POPC SOL > tau_t = 0.1 0.1 > ref_t = 300 300 > ref_p = 1 1 1 0 0 0 > tau_p = 10 > compressibility = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0 > This time my box size is reducing to 9.99065 9.99717 9.17646. > I cant figure out the problem. Any help will be appreciated. This suggests the same non-problem exists. Mark _______________________________________________ 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
