[gmx-users] Reg:walls and pbc xy
vinothkumar mohanakrishnan
kmvinoth at gmail.com
Tue Nov 2 11:28:36 CET 2010
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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