[gmx-users] Reg:walls and pbc xy
vinothkumar mohanakrishnan
kmvinoth at gmail.com
Wed Nov 3 06:41:42 CET 2010
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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>
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