Hi, With wall_r_linpot your wall potential is linear from 1 nm downwards. Since the LJ force is negative at 1 nm, your atoms are attracted to the walls.
But why not simply use two interfaces? You get double the sampling for free and you do not have to bother with complicated wall setups. Berk Date: Tue, 2 Nov 2010 11:49:48 +0530 From: [email protected] To: [email protected] Subject: [gmx-users] Reg:walls and pbc xy Hi Gromacians I want to create a liquid-liquid interface and study its properties. Hence i combined two boxes ( say water and DCE). The two boxes are well equilibrated before merging and i created an interface. Now i want to perform energy minimisation for the interface by appling pbc in the xy direction and using walls. ( If i apply pbc in all the directions i get two interfaces where as i need only one interface hence i am applying it only on the xy direction and removing the boundary condition in the Z direction.).When i performed the energy minimisation for the interfacial system but i found that my system is exploding (several PDB files are written while running mdrun is executed) and i dont know why?.There is no issue when i use pbc in all directions. below is my em.mdp file. any help is highly appreciated. integrator = steep emtol = 40.0 emstep = 0.01 nsteps = 10000 nstxout = 100 nstvout = 100 nstfout = 100 nstlog = 100 nstenergy = 100 nstlist = 5 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = Cut-off rvdw = 1.0 ewald_geometry = 3dc nwall = 2 wall_type = 9-3 wall_r_linpot = 1 wall_atomtype = opls_966 opls_968 wall_density = 9-3 9-3 wall_ewald_zfac = 3 pbc = xy fourierspacing = 0.18 Regards Vinoth -- 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
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