[gmx-users] Reg:walls and pbc xy

[vinothkumar mohanakrishnan]

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 <gmx3 at 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: kmvinoth at gmail.com
> To: gmx-users at 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
>
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