Hi, David van der Spoel I used the periodic boundary conditions. The box is 3.006x3.002x6.000 along x,y,z direction,respectively.The following is the em.mdp file.
; ; User xiao ; 2008.9.28 10:23 ; Input file ; cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = none integrator = steep nsteps = 20000 nstcomm = 1 ns_type = grid rlist = 0.8 coulombtype = cut-off rcoulomb = 1.2 vdwtype = cut-off rvdw = 1.2 Tcoupl = no Pcoupl = no gen_vel = no Please help me. Thanks again! H. Y. Xiao
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