Hi, Some comments below. I hope they help you On Mon, Jan 20, 2020 at 6:51 AM Pragati Sharma <pragati2...@gmail.com> wrote:
> Dear all, > > I want to calculate young's modulus of a polymer using uniaxial elongation. > (elongation in z axis but no volume change) > I am using 'deform' option and semiisotropic pressure coupling and zero > compressibility in z for that. My mdp parameters ar: > > *Pcoupl = BerendsenPcoupltype = > semiisotropictau_p = 1compressibility = 4.5e-5 > 0 compressibility = 4.5e-5 is the compressibility for water solution. Is this value also appropriate for the simulated system? > ref_p = 1 1gen_vel = nogen_temp > = 298; options for non-eq viscosity calcdeform = 0 0 0.001 0 > 0 0refcoord_scaling = com* > > Do you need refcoord_scaling? See for details http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=ref%20coord%20scaling#mdp-refcoord-scaling > Since elongation is in z axis, Lz increases, and Lx and Ly decreases, but > the decrease in these two axis is less compared to increase in Lz, and so > my volume is not conserved, it is increasing. > > The simulations are performed using the pressure coupling, thus controlling the pressure. I suggest to monitor the pressure along x and y to check if the simulation setting are appropriate. Are those values constant and at the desired values? > Can anyone suggest me some way for uniaxial elongation in gromacs, but > volume should not change > > Thanks! > Best regards Alessandra > -- > 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.