Hi, I have not heard about such issues, but it might depend a lot on your particular application. I would think you will always have disturbances, no matter if you use two interfaces, one interface with walls or one liquid-liquid interface and two liquid-vapour interfaces. The only solution to such problems is using thicker layers.
The wall are on the bottom (z=0) and top (z=z_box) of the box, as the manual says. Berk Date: Tue, 2 Nov 2010 14:59:31 +0530 Subject: Re: [gmx-users] Reg:walls and pbc xy From: kmvin...@gmail.com To: gmx-users@gromacs.org Hi Berk I need only one interface because if i have two interfaces the "capillary waves from one interface disturb the other even though the distance between the average positions of the two interfaces are larger than the potential cut-off" (this was said in the literature). Can anyone explain me why walls are used for interfaces? and what is the purpose of using walls?. suppose if i put nwall =2 where exactly are the walls created? can anyone explain me with an example? i read the manual but it is not making any sense to me. if i know this i know what correction i should make in my mdp file to make it work for pbc xy. any help is highly appreciated. Regards Vinoth On Tue, Nov 2, 2010 at 1:37 PM, Berk Hess <g...@hotmail.com> wrote: 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: kmvin...@gmail.com To: gmx-users@gromacs.org 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 gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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