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 <[email protected]> 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: [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 > > -- > 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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