# Two walls set up **URL:** \ **Category:** User discussions\ **Created:** [September 4, 2020, 1:26am UTC](https://gromacs.bioexcel.eu/t/two-walls-set-up/764 "2020-09-04T01:26:25Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![mijiddorj](https://avatars.discourse-cdn.com/v4/letter/m/779978/32.png) [@mijiddorj](https://gromacs.bioexcel.eu/u/mijiddorj)\ **Post date:** [September 4, 2020, 1:26am UTC](https://gromacs.bioexcel.eu/t/two-walls-set-up/764/1 "2020-09-04T01:26:26Z")
Dear Gmx users, Currently, I am working on membrane protein systems using CHARMM36 force field. I would like to use PBC for the x and y-axis and use the external electric field along the z-axis. I would like to restrict the PBC movement of ions along the z-axis. Can I use two walls in the CHARMM36 force field? Is there any possibility to use a vacuum slab? Best regards, Mijiddorj ---
**Author:** ![mijiddorj](https://avatars.discourse-cdn.com/v4/letter/m/779978/32.png) [@mijiddorj](https://gromacs.bioexcel.eu/u/mijiddorj)\ **Post date:** [September 27, 2020, 11:55pm UTC](https://gromacs.bioexcel.eu/t/two-walls-set-up/764/2 "2020-09-27T23:55:31Z")
I appreciate any comments. ---
**Author:** ![Dr\_DBW](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/dr_dbw/32/42_2.png) [@Dr\_DBW](https://gromacs.bioexcel.eu/u/Dr_DBW)\ **Post date:** [September 28, 2020, 7:08am UTC](https://gromacs.bioexcel.eu/t/two-walls-set-up/764/3 "2020-09-28T07:08:01Z")
Walls will introduce artifacts to the behaviour of all molecules/atoms. So that might not be what you really want to do. What exactly are you hoping to do to the ions? Keep them in an x-y plane? Individually, or all of them as a group? Keep them restrained into a thin x-y slab? Keep them around a particular point? ---
**Author:** ![mijiddorj](https://avatars.discourse-cdn.com/v4/letter/m/779978/32.png) [@mijiddorj](https://gromacs.bioexcel.eu/u/mijiddorj)\ **Post date:** [September 28, 2020, 7:46am UTC](https://gromacs.bioexcel.eu/t/two-walls-set-up/764/4 "2020-09-28T07:46:45Z")
Dear Dr. DBW, Thank you very much for your reply. I would like to perform MD simulation of pore structure in a membrane with the external electric field. 1. I would like to check the ion transfer through the pore. 2. The structural changes and dynamics of the peptide pore during the simulations. I actually tried short NVT simulations with the vacuum slabs top and bottom of the box around 1/3 of size along the z-axis. The system was equilibrated for 100 ns under 3D PBC condition. the mdp options were inserted as follows: pbc = xy nwall = 2 wall-type = 10-4 wall-density = 50 50 wall-atomtype = CA CA wall-r-linpot = 3 ewald-geometry = 3dc wall-ewald-zfac = 3 electric-field-z = 0.01 0 0 0 However, the simulations were stopped. Do you have any comment, please? ---
**Author:** ![Dr\_DBW](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/dr_dbw/32/42_2.png) [@Dr\_DBW](https://gromacs.bioexcel.eu/u/Dr_DBW)\ **Post date:** [September 28, 2020, 10:23pm UTC](https://gromacs.bioexcel.eu/t/two-walls-set-up/764/5 "2020-09-28T22:23:29Z")
Nothing other than “However, the simulations were stopped.” provides no information for people to be able to provide help. What command did you use? What was the output? Copy and paste the information, don’t type it out/filter it through your brain. ---
**Author:** ![mijiddorj](https://avatars.discourse-cdn.com/v4/letter/m/779978/32.png) [@mijiddorj](https://gromacs.bioexcel.eu/u/mijiddorj)\ **Post date:** [September 29, 2020, 12:22am UTC](https://gromacs.bioexcel.eu/t/two-walls-set-up/764/6 "2020-09-29T00:22:58Z")
Dear Dr. DBW, I am sorry for this inconsistency. 1. The command is: gmx mdrun -v -deffnm nvt -field for some options in mdp file * * * continuation = no constraint\_algorithm = lincs constraints = all-bonds lincs\_iter = 1 lincs\_order = 4 ; Neighborsearching cutoff-scheme = Verlet ns\_type = grid nstlist = 10 rlist = 1.2 rcoulomb = 1.2 rvdw = 1.2 ; Electrostatics coulombtype = PME pme\_order = 4 fourierspacing = 0.16 ; Temperature coupling is on tcoupl = V-rescale tc-grps = Protein\_DOPC Water\_and\_ions tau\_t = 0.1 0.1 ref\_t = 300 300 ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Dispersion correction DispCorr = EnerPres ; Velocity generation gen\_vel = yes gen\_temp = 300 gen\_seed = -1 ;nstcomm = 10 ;nstcalcenergy = 10 ;comm-mode = no ;Linear ;comm-grps = Protein\_DOPC Water\_and\_ions pbc = xy ; pbc in xy only nwall = 2 ; wall at z=0 and z=z-box wall-type = 10-4 ; direct 12-6 LJ as fn of distance from wall wall-density = 50 50 wall-atomtype = CA CA wall-r-linpot = 3 ewald-geometry = 3dc ; Only Ewald sum compatible with slab geometry, requires box\_height \>= slab\_height \* 3 wall-ewald-zfac = 3 ; Extra empty space for slab geometry calculation (reducing coulomb interaction) electric-field-z = 0.01 0 0 0 * * * The simulation was stopped at around 200 ps. The output error is as follows: * * * Program: gmx mdrun, version 2018.7 Source file: src/gromacs/mdlib/nbnxn\_grid.cpp (line 402) Software inconsistency error: Lost particles while sorting For more information and tips for troubleshooting, please check the GROMACS website at [http://www.gromacs.org/Documentation/Errors](http://www.gromacs.org/Documentation/Errors) * * * Thank you very much for your time. Best regards, Mijiddorj ---
**Author:** ![di\_jin](https://avatars.discourse-cdn.com/v4/letter/d/e274bd/32.png) [@di\_jin](https://gromacs.bioexcel.eu/u/di_jin)\ **Post date:** [November 29, 2020, 3:45pm UTC](https://gromacs.bioexcel.eu/t/two-walls-set-up/764/7 "2020-11-29T15:45:41Z")
Hi, I encountered the exact same issue. The solution for me was to use gmx editconf -box to make the box bigger in the z-direction such that there are some vacuum space above and below the system. This will make sure that there are no atom within the artificial wall. Try it, and hopefully it will work for you too. ---
**Author:** ![mijiddorj](https://avatars.discourse-cdn.com/v4/letter/m/779978/32.png) [@mijiddorj](https://gromacs.bioexcel.eu/u/mijiddorj)\ **Post date:** [December 11, 2020, 1:43am UTC](https://gromacs.bioexcel.eu/t/two-walls-set-up/764/8 "2020-12-11T01:43:40Z")
Dear Di\_jin, Thank you very much for your kind reply. Best regards, Mijiddorj ---
**Author:** ![Priya](https://avatars.discourse-cdn.com/v4/letter/p/eada6e/32.png) [@Priya](https://gromacs.bioexcel.eu/u/Priya)\ **Post date:** [June 20, 2023, 10:18pm UTC](https://gromacs.bioexcel.eu/t/two-walls-set-up/764/9 "2023-06-20T22:18:39Z")
Hi , I want to know atom type “CA” means what? ---
**Author:** ![Kaustubh](https://avatars.discourse-cdn.com/v4/letter/k/45deac/32.png) [@Kaustubh](https://gromacs.bioexcel.eu/u/Kaustubh)\ **Post date:** [March 12, 2024, 3:08pm UTC](https://gromacs.bioexcel.eu/t/two-walls-set-up/764/10 "2024-03-12T15:08:03Z")
Hope you issue has been sorted out by now. CA, in this case, might be the customized atomtype or the calcium ion (denoted as CA in OPLS-AA) employed to represent walls.