Dear gmx-users,<br>I do a minimization run with this mdp:<br>-----------------------------<br>constraints = none<br>;define = -DFLEX_SPC<br>integrator = cg<br>;nstcgsteep = 300<br>emtol = 100.0<br>
emstep = 0.005<br>dt = 0.001 ; ps !<br>nsteps = 200000 ; total 200 ps.<br>nstcomm = 100<br>nstxout = 10000<br>nstvout = 0<br>nstfout = 0<br>
nstlog = 10000<br>nstenergy = 1000<br>nstlist = 10<br>ns_type = grid<br>rlist = 1.0<br>rcoulomb = 1.0<br>rvdw = 1.0<br>coulombtype = PME ; Reaction-Field<br>
fourierspacing = 0.12<br>pme_order = 4<br>optimize_fft = yes<br>;epsilon_r = 1.0<br>; Berendsen temperature coupling is on in two groups<br>Tcoupl = berendsen<br>tc-grps = Protein SOL<br>
tau_t = 0.01 0.01<br>ref_t = 310 310<br>; Energy monitoring<br>energygrps = Protein SOL<br>; Isotropic pressure coupling is now on<br>Pcoupl = berendsen<br>Pcoupltype = isotropic<br>
tau_p = 0.25<br>compressibility = 5.4e-5<br>ref_p = 1.0<br>; Generate velocites is off at 300 K.<br>gen_vel = no<br>;gen_temp = 300.0<br>;gen_seed = 749261<br>
<br>---------------------------<br>and get the error, output like this:<br><br>Polak-Ribiere Conjugate Gradients:<br> Tolerance (Fmax) = 1.00000e+02<br> Number of steps = 200000<br> F-max = 4.69437e+04 on atom 2513<br>
F-Norm = 1.05294e+03<br><br><br>step -1: Water molecule starting at atom 43372 can not be settled.<br>Check for bad contacts and/or reduce the timestep if appropriate.<br><br>...<br><br>Fatal error:<br>1 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y.<br>
This usually means that your system is not well equilibrated.<br>--------------------------<br><br>I did a successful run with another equivalent system (same protein sequence, same number of atoms), even with a LARGER TIMESTEP, 0.002 ps<br>
I found a lot of people encounter the same error, but in production run step. And in those cases, they're advised to minimize/equilibrate the system more thoroughly. What can I do to resolve this problem in MINIMIZATION step?<br>
<br>Many thanks<br>Trang<br><br>