# Problem while applying pressure coupling on a system containing frozen slab **URL:** \ **Category:** User discussions\ **Tags:** mdp-parameters\ **Created:** [June 13, 2024, 7:13am UTC](https://gromacs.bioexcel.eu/t/problem-while-applying-pressure-coupling-on-a-system-containing-frozen-slab/9372 "2024-06-13T07:13:50Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![Arkaja](https://avatars.discourse-cdn.com/v4/letter/a/ac91a4/32.png) [@Arkaja](https://gromacs.bioexcel.eu/u/Arkaja)\ **Post date:** [June 13, 2024, 7:13am UTC](https://gromacs.bioexcel.eu/t/problem-while-applying-pressure-coupling-on-a-system-containing-frozen-slab/9372/1 "2024-06-13T07:13:50Z")
GROMACS version: VERSION 2024.2-Homebrew GROMACS modification: Yes/No I have a simulation box of dimensions 70x70x600 Ang^3, containing, a solid slab (70x70x100) in middle of box (whose atoms are frozen) and there is water (liquid) on both of the outer surfaces. I am performing NPAzT simulations. While applying npt, I want to compress the box from both sides in z direction but the box size is changing in only in one direction (extreme right box boundary is changing), however I did’nt see any changes in the left box boundary. I understand it could be because of shifting of box origin to 0 during pressure scaling however the coordinates of the surface is not changing (because of freeze command that I have applied). After running simulations, the right side water molecules which were initially adsorb onto the slab are getting desorbed and moving away from the surface while the water remains adsorbed on the slab on the left side. I want to keep the surface frozen and want to applying pressure scaling in z direction. What should I do? I want to ensure that the pressure should apply in both direction. Here are the mdp parameters which I have given:- ;NPT input file ;------------------------------------ integrator = md ; dt = 0.002 ; in ps nsteps =5000 ; ;------Names of freeze group freezegrps = CCT ; freezing Calcite freezedim = Y Y Y ; freezing in all directions ;------- Continuation ;continuation = no ; by default tinit = 0 ; starting t value in ps, ;------- Output printing nstcalcenergy = 100 ; calculating energy freq nstenergy = 500 ; energy output frequency in edr nstlog = 500 ; energy output frequency in log nstxout-compressed = 500 ; trajectory output frequency (output is .xtc file) nstcomm = 100 ; nstcomm = nstcalcenergy (gmx note) ;------- Generate velocities is off gen\_vel = yes gen\_temp = 300 nstlist = 100 ;default ;---------bond constraints constraint\_algorithm = lincs ; holonomic constraints constraints = h-bonds ; all h containing bonds (even heavy atom-H bonds) lincs\_iter = 4 ; accuracy of LINCS (default) lincs\_order = 8 ; also related to accuracy (default) lincs\_warnangle = 90 ; ;------Wall Parameters ;nwall = 2 ;wall-atomtype = mmsl\_900 mmsl\_900 ;wall-type = 12-6 ;ewald-geometry = 3dc ;------LJ and electrostatic interaction cutoff-scheme = Verlet ; integrator verlet-buffer-tolerance = -1 vdwtype = Cut-off ; cut-off by default rvdw = 1.2 ; vdw cut-off vdw-modifier = none coulombtype = PME ; Ewald type pme\_order = 4 ; cubic interpolation (bydefault) rcoulomb = 1.2 ; cutoff coulomb-modifier = none fourierspacing = 0.12 ; grid spacing for FFT (bydefault) ewald\_rtol = 1e-6 ; (bydefault) rlist = 1.4 ;----------dispcorrection DispCorr = Ener ;----------PBC pbc = xyz ; pbc only in two direction ;----------------Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = CCT HEP TOL ; multiple coupling groups - more accurate tau\_t = 0.1 0.1 0.1 ; time constant, in ps ref\_t = 300 300 300 ; reference temperature, one for each group, in K ;----------------Presure Coupling pcoupl = Parrinello-Rahman pcoupltype = anisotropic ;xx, yy, zz, xy/yx, xz/zx and yz/zy compressibility = 0.0 0.0 4.5e-11 0.0 0.0 0.0 ref-p = 0.0 0.0 1.0 0.0 0.0 0.0 tau-p = 2.0 ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [June 14, 2024, 9:03am UTC](https://gromacs.bioexcel.eu/t/problem-while-applying-pressure-coupling-on-a-system-containing-frozen-slab/9372/2 "2024-06-14T09:03:36Z")
With freeze groups such issues can not be avoided completely, but you can translate your system such that the slab is just above z=0. That will minimize the artifacts. Another solution could be to use position restraints with refcoord-scaling=com.