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