Hello, I am compressing a single extended PE chain (16 nm in length) in a box of 20nm in vacuo to get a more realistic shape of the polymer. Although system is small (only 362 atoms), whatever -np # I choose simulation runs very slowly. Is that because of the presence of voids? Is there a way to speed up the runs? I have no clue on this. Thanks!
(mpirun -np 4 mdrun_mpi ....... -pd) starting mdrun 'Polymer' 1000000 steps, 2000.0 ps. step 0 step 100, will finish Thu Mar 24 19:33:34 2011 step 200, will finish Thu Mar 24 19:29:18 2011 step 300, will finish Thu Mar 24 19:27:42 2011 step 400, will finish Thu Mar 24 19:27:13 2011 step 500, will finish Thu Mar 24 19:27:54 2011 pbc = xyz ; Run control integrator = md dt = 0.002 nsteps = 1000000 ;5000 nstcomm = 100 ; Output control nstenergy = 100 nstxout = 100 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 1000 ; Neighbor searching nstlist = 10 ns_type = grid ; Electrostatics/VdW coulombtype = PME vdw-type = Shift rcoulomb-switch = 0 rvdw-switch = 0.9 ;0 ; Cut-offs rlist = 1.25 rcoulomb = 1.25 ;1.1 rvdw = 1.0 ; PME parameters fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 ;optimize_fft = yes ; Temperature coupling Tcoupl = v-rescale tc-grps = System tau_t = 0.1 ref_t = 300 ; Pressure coupling Pcoupl = berendsen;Parrinello-Rahman Pcoupltype = isotropic tau_p = 0.5 0.5 compressibility = 4.5e-5 4.5e-5 ref_p = 10 10 ; Velocity generation gen_vel = yes gen_temp = 300.0 gen_seed = 173529 ; Bonds constraints = none;all-bonds constraint-algorithm = lincs
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