| Hi all, In the TIP4P water layer above my dmpc bilayer after 100ps (OPLS-BERGER) a hole is being formed. Some water molecules are absent in the water layer, but the total no of water molecules are same. This is my semi.mdp file title = bilayer MD DMPC PURE cpp = /usr/bin/cpp define = -DDMPC_POSRES constraints = all-bonds constraint_algorithm= lincs lincs_order = 4 lincs_warnangle = 30 integrator = md dt = 0.002 ; ps ! nsteps = 1000000 ; total 1 ns. nstcomm = 1 comm-mode = linear nstxout = 500 nstvout = 500 nstfout = 500 nstenergy = 100 nstlist = 5 ns_type = grid rlist = 1.0 rcoulomb = 1.0 vdwtype = Cut-off rvdw = 1.4 pbc = xyz fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 coulombtype = PME pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tau_t = 0.1 0.1 tc-grps = DMPC SOL ref_t = 300 300 ; Pressure coupling is not on Pcoupl = berendsen tau_p = 5.0 5.0 compressibility = 4e-5 4.5e-5 ref_p = 1.0 1.0 pcoupltype = semiisotropic ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529awaiting your help |
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