Hi, On Thu, Nov 28, 2019 at 1:23 PM Pragati Sharma <pragati2...@gmail.com> wrote:
> Hello users, > > I am trying to plot stress-strain curve for natural rubber from NPT > simulations using the "deform" option. Deform along x direction at 1 bar > pressure. The parameters I gave in mdp file are: > > Pcoupl = Berendsen > Pcoupltype = semiisotropic > tau_p = 2 > compressibility = 0 4.5e-5 4.5e-5 > ref_p = 1 1 1 > deform = 0.01 0 0 0 0 0 > > Q. Should I give six values to ref_P and compressibility also. > Semiisotropic: Pressure coupling which is isotropic in the x and y direction, but different in the z direction. Two values each for compressibility and ref-p are required, for x/y and z directions respectively. Anisotropic: values are needed for xx, yy, zz, xy/yx, xz/zx and yz/zy components, respectively. When the off-diagonal compressibilities are set to zero, a rectangular box will stay rectangular. Beware that anisotropic scaling can lead to extreme deformation of the simulation box. Best regards Alessandra Q. If I give 'anisotropic' coupling, then the error is > "ERROR 1: Pressure coupling incorrect number of values (I need exactly 6)" > Should I give the next three values as zero or 1. OR I can just use > semiisotropic coupling only. > > Thanks in advance!! > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.