[gmx-users] Reg:walls and pbc xy

Berk Hess gmx3 at hotmail.com
Tue Nov 2 09:07:19 CET 2010


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.


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      


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