Hi,<br><br>I am trying to simulate a system of 880 particles with implicit solvent using brownian dynamics, but the simulation generates huge log files (it writes md.log files at a rate of almost 5MB/minute) and this crashed my system since I ran out of space :(<br>
<br>My mdp file looks like this:<br><br>include =<br>define =<br>integrator = bd<br>tinit = 0<br>dt = 0.001<br>nsteps = 100000000 ;100000<br>
simulation_part = 1<br>init_step = 0<br>comm-mode = Angular<br>nstcomm = 1<br>comm-grps =<br><br>emtol = 0.01<br>emstep = 1.5<br>
<br>nstxout = 10000<br>nstvout = 10000<br>nstfout = 10000<br><br>nstenergy = 1000<br><br>nstxtcout = 1000<br>xtc-precision = 1000<br>
<br>nstlog = 0<br><br>xtc-grps =<br>energygrps =<br><br>ns_type = grid<br>pbc = xyz<br>periodic_molecules = no<br><br>rlist = 8.95<br>
<br>coulombtype = user<br>rcoulomb-switch = 0<br>rcoulomb = 8.95<br>epsilon-r = 1<br><br>vdw-type = user ;cutoff<br>rvdw-switch = 0<br>rvdw = 8.95<br>
DispCorr = No<br>table-extension = 1<br><br>; Seperate tables between energy group pairs<br>energygrps = A T G C P300 SA SB<br><br><br>energygrp_table = A A A T A G A C A P300 A SA A SB T T T G T C T P300 T SA T SB G G G C G P300 G SA G SB C C C P300 C SA C SB P300 P300 P<br>
300 SA P300 SB SA SA SA SB SB SB<br><br>; Spacing for the PME/PPPM FFT grid<br>fourierspacing = 0.10<br><br>Tcoupl = Nose-Hoover<br>tc-grps = System<br>tau_t = 0.001<br>
ref_t = 300.00<br><br>Pcoupl = No<br><br>andersen_seed = 815131<br><br>gen_vel = yes<br>gen_temp = 300.0000<br>gen_seed = 1993<br>
<br>Please let me know if there is a solution to write smaller mdp files. I have set nstlog = 0 , but even that doesn't work!<br><br>Thanks<br>Nimesh<br><br><br>