Dear Justin and Mark, My pr.mdp file is: title = pr.mdp cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 nsteps =100000 nstcomm = 1 nstxout = 250 nstvout = 1000 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e5 optimize_fft = yes ;Berendsen temperature coupling is on Tcoupl = berendsen tau_t = 0.1 0.1 0.1 tc-grps = protein SOL NA+ ref_t = 298 298 298 ;Pressure coupling is on Pcoupl = berendsen tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ;Generate velocities is on at 298 K gen_vel = yes gen_temp = 298 gen_seed = 173529
As the warning is : Step 1 Warning: pressure scaling more than 1%, mu: -2.6855e+10 -2.6855e+10 -2.6855e+10 As the pressure is high so it shoud be how much? Regards, Lal badshah Send instant messages to your online friends http://uk.messenger.yahoo.com
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