[gmx-users] Reg:walls and pbc xy

Sander Pronk pronk at cbr.su.se
Wed Nov 3 09:04:23 CET 2010


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 <kmvinoth at 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 <gmx3 at 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: 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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