<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div>Dear all,<br><br>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:<br><br>cpp = /usr/bin/cpp<br>constraints = hbonds<br>integrator = md<br>dt = 0.002 ; ps !<br>nsteps = 100000000 ;.<br>nstxout = 50000 ; <br>nstxtcout = 1000<br>nstvout = 0<br>nstfout = 0<br>nstlog = 100<br>nstenergy = 1000<br>nstlist = 5<br>ns_type = grid<br>rlist = 1.2<br>coulombtype = PME<br>rcoulomb = 1.2<br>rvdw = 1.2<br>fourierspacing = 0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4<br>ewald_rtol = 1e-5<br>optimize_fft = yes<br>Tcoupl = Nose-Hoover<br>tc-grps = Protein lipid SOL_Ion<br>tau_t = 0.5 0.5 0.5 <br>ref_t = 310 310 310<br>;Pressure coupling is on<br>pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT<br>pcoupltype =
semiisotropic ; uniform scaling of x-y box vectors, independent z<br>tau_p = 1.0 1.0 ; time constant, in ps<br>ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar)<br>compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1<br><br>gen_vel = no<br>gen_temp = 310.0<br>gen_seed = 173529<br><br>nstcomm = 5<br>comm-mode = Linear<br>comm-grps = Protein_lipid SOL_Ion<br>; put two walls<br>pbc = xy<br>ewald_geometry
= 3dc<br>nwall = 2<br>wall_atomtype = C C<br>wall_type = 12-6<br>wall_ewald_zfac = 3<br>wall_r_linpot = 0.5<br><br>Thanks very much!<br><br>Cheers,<br><br>Jianguo<br>Postdoc,<br>BII&SERI,<br>Singapore<br><br></div>
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