[gmx-users] Reg:walls and pbc xy
Berk Hess
gmx3 at hotmail.com
Tue Nov 2 11:11:42 CET 2010
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: kmvinoth at gmail.com
To: gmx-users at 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 <gmx3 at 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: kmvinoth at gmail.com
To: gmx-users at 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 <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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