Dear all, I was trying to add two walls at z=0 and z=z_box to my system which contains one peptide and one membrane. Since I am interested in how the peptides affect membrane properties (i.e., area per lipid), I need to use semi-isotropic pressure coupling. But I wanted to mimick the two-dimensional periodicity of the membrane and thus don't want to include the z-component of the ewald summation, so I decided to add two walls so that I can use ewald_geometry=3dc. Since there is no periodicity in z dimension, I kept two regions up and below the membrane neutral. However, when the simulation proceeds, the box length in z dimemsion keep increasing and results in a large vacum between image boxes in z dimension. Could anyone help me figure out what's going wrong? The following is my mdp file and I will be glad to provide any other details if needed:
cpp = /usr/bin/cpp constraints = hbonds integrator = md dt = 0.002 ; ps ! nsteps = 100000000 ;. nstxout = 50000 ; nstxtcout = 1000 nstvout = 0 nstfout = 0 nstlog = 100 nstenergy = 1000 nstlist = 5 ns_type = grid rlist = 1.2 coulombtype = PME rcoulomb = 1.2 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes Tcoupl = Nose-Hoover tc-grps = Protein lipid SOL_Ion tau_t = 0.5 0.5 0.5 ref_t = 310 310 310 ;Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 1.0 1.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1 gen_vel = no gen_temp = 310.0 gen_seed = 173529 nstcomm = 5 comm-mode = Linear comm-grps = Protein_lipid SOL_Ion ; put two walls pbc = xy ewald_geometry = 3dc nwall = 2 wall_atomtype = C C wall_type = 12-6 wall_ewald_zfac = 3 wall_r_linpot = 0.5 Thanks very much! Cheers, Jianguo Postdoc, BII&SERI, Singapore
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