<font size="4">Dear gmx users,</font><div><font size="4"><br></font></div><div><font size="4">I tried to do simulations of a small peptide in vacuum, I found that it failed to be run in parallel, even when I use only 8 cores.</font></div>
<div><font size="4">My system only have hundreds of atoms. the problem may be resulted from domain decomposition. When I choose particle</font></div><div><font size="4">decomposition method, for small system, I can use 4 threads but not 8, and for a little bigger systems, I can only use 8 threads.</font></div>
<div><font size="4"><br></font></div><div><font size="4">For this situation, is it normal? Is there some solution to this problem? Thanks very much!</font></div><div><font size="4"><br></font></div><div><font size="4">The following lines are my mdp file for the vacuum simulation:</font></div>
<div><br></div><div><span style="background-color:rgb(255,255,0)"> title = PDXN of Abeta in H2O</span><div><span style="background-color:rgb(255,255,0)">;cpp = /lib/cpp ; prepocessor of the current machine</span></div>
<div><span style="background-color:rgb(255,255,0)">define = ;-DPOSRES </span></div><div><span style="background-color:rgb(255,255,0)">integrator = md ; molecular dynamics algorithm</span></div>
<div><span style="background-color:rgb(255,255,0)">tinit = 0.0 ; start time and timestep in ps</span></div><div><span style="background-color:rgb(255,255,0)">dt = 0.002 ; time step in ps</span></div>
<div><span style="background-color:rgb(255,255,0)">nsteps = 500000000 ; number of steps for 1000ns run</span></div><div><span style="background-color:rgb(255,255,0)">emtol = 100 ; convergence criterion</span></div>
<div><span style="background-color:rgb(255,255,0)">emstep = 0.05 ; intial step size</span></div><div><span style="background-color:rgb(255,255,0)">nstlist = 10 ; step frequency for updating neighbour list</span></div>
<div><span style="background-color:rgb(255,255,0)">ns_type = grid ;simple ; method for neighbour searching (?)</span></div><div><span style="background-color:rgb(255,255,0)">nstxout = 5000 ; frequency for writing coords to output .trr file</span></div>
<div><span style="background-color:rgb(255,255,0)">nstvout = 0 ; frequency for writing velocities to output...should be same as nstxout</span></div><div><span style="background-color:rgb(255,255,0)">nstfout = 0 ; frequency for writing forces to output</span></div>
<div><span style="background-color:rgb(255,255,0)">nstlog = 5000 ; frequency for writing energies to log file</span></div><div><span style="background-color:rgb(255,255,0)">nstenergy = 5000 ; frequency for writing energies to energy file</span></div>
<div><span style="background-color:rgb(255,255,0)">nstxtcout = 5000 ; frequency for writing coords to xtc traj</span></div><div><span style="background-color:rgb(255,255,0)">xtc_grps = system ; group(s) whose coords are to be written in xtc traj</span></div>
<div><span style="background-color:rgb(255,255,0)">energygrps = system ; group(s) whose energy is to be written in energy file</span></div><div><span style="background-color:rgb(255,255,0)">pbc = no ; use pbc</span></div>
<div><span style="background-color:rgb(255,255,0)">rlist = 0 ; cutoff lengths (nm)</span></div><div><span style="background-color:rgb(255,255,0)">epsilon_r = 1.0 ; Dielectric constant (DC) for twin-range or DC of reaction field</span></div>
<div><span style="background-color:rgb(255,255,0)">niter = 100 ; Some thingies for future use </span></div><div><span style="background-color:rgb(255,255,0)">fourierspacing<span class="Apple-tab-span" style="white-space:pre"> </span> = 0.16</span></div>
<div><span style="background-color:rgb(255,255,0)">fourier_nx = 30</span></div><div><span style="background-color:rgb(255,255,0)">fourier_ny = 30</span></div><div><span style="background-color:rgb(255,255,0)">fourier_nz = 30</span></div>
<div><span style="background-color:rgb(255,255,0)">coulombtype = Cut-off ; truncation for minimisation, with large cutoff</span></div><div><span style="background-color:rgb(255,255,0)">rcoulomb = 0</span></div>
<div><span style="background-color:rgb(255,255,0)">rcoulomb-switch = 0</span></div><div><span style="background-color:rgb(255,255,0)">vdw-type = Cut-off ; truncation for minimisation, with large cutoff</span></div>
<div><span style="background-color:rgb(255,255,0)">rvdw-switch = 0</span></div><div><span style="background-color:rgb(255,255,0)">rvdw = 0 ; cut-off lengths</span></div><div><span style="background-color:rgb(255,255,0)">;pme_order = 6 ; EWALD/PME/PPPM parameters</span></div>
<div><span style="background-color:rgb(255,255,0)">;ewald_rtol = 1e-05</span></div><div><span style="background-color:rgb(255,255,0)">;ewald_geometry = 3d</span></div><div><span style="background-color:rgb(255,255,0)">epsilon_surface = 0</span></div>
<div><span style="background-color:rgb(255,255,0)">optimize_fft = yes</span></div><div><span style="background-color:rgb(255,255,0)"> Free energy control stuff</span></div><div><span style="background-color:rgb(255,255,0)">free_energy = yes</span></div>
<div><span style="background-color:rgb(255,255,0)">init_lambda = 0.0</span></div><div><span style="background-color:rgb(255,255,0)">delta_lambda = 0</span></div><div><span style="background-color:rgb(255,255,0)">sc_alpha =0.5</span></div>
<div><span style="background-color:rgb(255,255,0)">sc-power =1.0</span></div><div><span style="background-color:rgb(255,255,0)">sc-sigma = 0.3</span></div><div><span style="background-color:rgb(255,255,0)">comm_mode = angular</span></div>
<div><span style="background-color:rgb(255,255,0)">nstcomm = 10 ; number of steps for centre of mass motion removal (in vacuo only!)</span></div><div><span style="background-color:rgb(255,255,0)">Tcoupl = V-rescale</span></div>
<div><span style="background-color:rgb(255,255,0)">tc_grps = system ; MVN_Protein ;SOL_Ion ; Non-Protein </span></div><div><span style="background-color:rgb(255,255,0)">tau_t = 0.01 </span></div>
<div><span style="background-color:rgb(255,255,0)">ref_t = 300</span></div><div><span style="background-color:rgb(255,255,0)">Pcoupl = no ; Parrinello-Rahman ; Pressure coupling </span></div>
<div><span style="background-color:rgb(255,255,0)">;Pcoupltype = Isotropic</span></div><div><span style="background-color:rgb(255,255,0)">;tau_p = 1.0 1.0 1.0</span></div><div><span style="background-color:rgb(255,255,0)">;ref_p = 1.0 1.0 1.0</span></div>
<div><span style="background-color:rgb(255,255,0)">;compressibility = 4.5e-5 ; compressibility</span></div><div><span style="background-color:rgb(255,255,0)">;</span></div><div><span style="background-color:rgb(255,255,0)">annealing = no ; SIMULATED ANNEALING CONTROL </span></div>
<div><span style="background-color:rgb(255,255,0)">;zero_temp_time = 0 ; Time at which temperature should be zero (ps)</span></div><div><span style="background-color:rgb(255,255,0)">gen_vel = yes</span></div>
<div><span style="background-color:rgb(255,255,0)">gen_temp = 300</span></div><div><span style="background-color:rgb(255,255,0)">gen_seed = -1</span></div><div><span style="background-color:rgb(255,255,0)">constraints = all-bonds ; OPTIONS FOR BOND CONSTRAINTS </span></div>
<div><span style="background-color:rgb(255,255,0)">constraint-algorithm = Lincs ; Type of constraint algorithm</span></div><div><span style="background-color:rgb(255,255,0)">lincs_order = 4 ; Highest order in the expansion of the constraint coupling matrix</span></div>
<div><span style="background-color:rgb(255,255,0)">lincs_iter = 1</span></div><div><span style="background-color:rgb(255,255,0)">lincs_warnangle = 30 ; Lincs will write a warning to the stderr if in one step a bond rotates </span></div>
<div><span style="background-color:rgb(255,255,0)"> ; over more degrees than </span></div><div><span style="background-color:rgb(255,255,0)">unconstrained-start = no ; Do not constrain the start configuration</span></div>
<div><span style="background-color:rgb(255,255,0)">;Shake-SOR = no ; Use successive overrelaxation to reduce the number of shake iterations</span></div><div><span style="background-color:rgb(255,255,0)">;shake-tol = 1e-04 ; Relative tolerance of shake</span></div>
<div><span style="background-color:rgb(255,255,0)">morse = no ; Convert harmonic bonds to morse potentials</span></div><div><br></div><div><br></div>-- <br>Best Regards,<div><br></div><div>Qinghua</div>
<div><br></div><br>
</div>