Hello,<br><br>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!<br>
<br>(mpirun -np 4 mdrun_mpi ....... -pd)<br><br>starting mdrun 'Polymer'<br>1000000 steps, 2000.0 ps.<br>step 0<br>step 100, will finish Thu Mar 24 19:33:34 2011<br>step 200, will finish Thu Mar 24 19:29:18 2011<br>
step 300, will finish Thu Mar 24 19:27:42 2011<br>step 400, will finish Thu Mar 24 19:27:13 2011<br>step 500, will finish Thu Mar 24 19:27:54 2011<br><br><br><br>pbc = xyz <br> <br>; Run control <br>
integrator = md <br>dt = 0.002 <br>nsteps = 1000000 ;5000 <br>nstcomm = 100 <br><br>; Output control<br>
nstenergy = 100 <br>nstxout = 100 <br>nstvout = 0<br>nstfout = 0<br>nstlog = 1000 <br>nstxtcout = 1000 <br>
<br>; Neighbor searching<br>nstlist = 10 <br>ns_type = grid <br><br>; Electrostatics/VdW <br>coulombtype = PME <br>vdw-type = Shift <br>
rcoulomb-switch = 0 <br>rvdw-switch = 0.9 ;0 <br><br>; Cut-offs<br>rlist = 1.25 <br>rcoulomb = 1.25 ;1.1 <br>rvdw = 1.0 <br>
<br>; PME parameters<br>fourierspacing = 0.12 <br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4 <br>ewald_rtol = 1e-5<br>
;optimize_fft = yes<br><br>; Temperature coupling <br>Tcoupl = v-rescale <br>tc-grps = System <br>tau_t = 0.1 <br>ref_t = 300 <br>
<br>; Pressure coupling<br>Pcoupl = berendsen;Parrinello-Rahman <br>Pcoupltype = isotropic <br>tau_p = 0.5 0.5 <br>compressibility = 4.5e-5 4.5e-5 <br>
ref_p = 10 10 <br><br>; Velocity generation <br>gen_vel = yes <br>gen_temp = 300.0 <br>gen_seed = 173529 <br>
<br>; Bonds<br>constraints = none;all-bonds <br>constraint-algorithm = lincs<br><br>