The walls are simply interactions between the atomtype of the wall you specified (in your case opls_966 and opls_968), and the rest of the system, at the planes defined by z=0 or z=z_box.
> wall_type = 9-3 > wall_r_linpot = 1 > wall_atomtype = opls_966 opls_968 > wall_density = 9-3 9-3 > wall_ewald_zfac = 3 There seems to be a problem with your 'wall_density' setting, though. They serve as scalar multipliers of the interaction strength, so they should be numbers. One reason things might be blowing up is if there are strong forces: when atoms are too close to the wall. Sander On Nov 3, 2010, at 06:41 , vinothkumar mohanakrishnan wrote: > Hi all > > Can anyone help me out with the wall settings for running above mentioned > liquid-liquid interface. with the mdp file i have my system is exploding. any > help is highly appreciated. > > Regards > Vinoth > > On Tue, Nov 2, 2010 at 3:58 PM, vinothkumar mohanakrishnan > <kmvin...@gmail.com> wrote: > Hi Berk > > Thank you. what settings i should change in mdp file (energy minimisation) to > run the energy minimisation for the single liquid-liquid interface > (liquid-vapour interface at the other two extremes) without any issues? > kindly be specific ( what parameter i should change) below is my 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 > > On Tue, Nov 2, 2010 at 3:41 PM, Berk Hess <g...@hotmail.com> wrote: > I meant to say that if you see effects of one interface on another with a > layer of 1 nm thickness/height, > these effects will be less with a layer of 2 nm thickness and even less with > 10 nm thickness. > > Berk > > Date: Tue, 2 Nov 2010 15:30:34 +0530 > > Subject: Re: [gmx-users] Reg:walls and pbc xy > From: kmvin...@gmail.com > To: gmx-users@gromacs.org > > Hi Berk > > Thank you once again. How can i use thick layers and what is the procedure? > can you explain it bit more on this? > > Regards > Vinoth > > On Tue, Nov 2, 2010 at 3:18 PM, Berk Hess <g...@hotmail.com> wrote: > 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! 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