Hi Gromacs users,<div><br></div><div>My invocation of mdrun, using 8 processors and the following mdp file:</div><div><br></div><div><br></div><div><div>title = Alkanethiol SAM MD</div><div>; Run parameters</div>
<div>integrator = md ; leap-frog integrator</div><div>nsteps = 500000 ; 25 * 40 = 1000 ps, 1 ns (actually .2ns now)</div><div>dt = 0.001 ; .5 fs (changed from 2.5)</div>
<div>; Output control</div><div>nstxout = 1 ; save coordinates every 2 ps</div><div>nstvout = 100 ; save velocities every 2 ps</div><div>nstxtcout = 100 ; xtc compressed trajectory output every 2 ps</div>
<div>nstenergy = 100 ; save energies every 2 ps</div><div>nstlog = 100 ; update log file every 2 ps</div><div>nstfout = 100 ; save forces every .1 ps</div><div>; Bond parameters</div>
<div>continuation = yes ; Restarting after NPT</div><div>constraint_algorithm = lincs ; holonomic constraints</div><div>constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained</div>
<div>lincs_iter = 1 ; accuracy of LINCS</div><div>lincs_order = 4 ; also related to accuracy</div><div>; Neighborsearching</div><div>ns_type = grid ; search neighboring grid cells</div>
<div>nstlist = 5 ; 10 fs</div><div>rlist = 1.4 ; short-range neighborlist cutoff (in nm)</div><div><div>coulombtype = Cut-off</div><div>rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)</div>
<div>rvdw = 1.4 ; short-range van der Waals cutoff (in nm)</div><div>; Electrostatics</div><div>pme_order = 4 ; cubic interpolation</div><div>fourierspacing = 0.16 ; grid spacing for FFT</div>
<div>; ewald summation</div><div>; Temperature coupling is on</div><div>tcoupl = V-rescale ; modified Berendsen thermostat</div><div>tc-grps = System ; two coupling groups - more accurate</div>
<div>tau_t = 0.1 ; time constant, in ps</div><div>ref_t = 300 ; reference temperature, one for each group, in K</div><div>; Pressure coupling is on</div><div>;pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT</div>
<div>;pcoupltype = isotropic ; uniform scaling of box vectors</div><div>;tau_p = 2.0 ; time constant, in ps</div><div>;ref_p = 1.0 ; reference pressure, in bar</div><div>;compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1</div>
<div>; Periodic boundary conditions</div><div>pbc = xyz ; 3-D PBC</div><div>; Dispersion correction</div><div>DispCorr = EnerPres ; account for cut-off vdW scheme</div><div>; Velocity generation</div>
<div>gen_vel = no ; Velocity generation is off</div><div>; Non-equilibrium MD</div><div>freezegrps = S DIO</div><div>freezedim = Y Y Y N N Y ; frozen in all three dimensions</div><div>
<br></div></div></div><div><br></div><div><br></div><div>generated the following error message:</div><div><br></div><div><div><br></div><div><br></div><div><div>There are: 1184 Atoms</div><div>Charge group distribution at step 0: 30 36 45 54 180 211 216 252 30 34 45 51</div>
<div>Grid: 3 x 4 x 4 cells</div><div>Initial temperature: 0 K</div><div><br></div><div>Started mdrun on node 0 Fri Apr 20 08:41:31 2012</div><div><br></div><div> Step Time Lambda</div><div> 0 0.00000 0.00000</div>
<div><br></div><div> Energies (kJ/mol)</div><div> Angle Ryckaert-Bell. LJ-14 Coulomb-14 LJ (SR)</div><div> 3.19470e+03 8.21460e+00 8.87579e+01 0.00000e+00 -5.95420e+03</div><div>
Disper. corr. Coulomb (SR) Potential Kinetic En. Total Energy</div><div> -1.10584e+01 0.00000e+00 -2.67358e+03 1.60252e+03 -1.07106e+03</div><div> Conserved En. Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd</div>
<div> -1.07106e+03 1.76581e+02 -5.03783e-01 -3.74984e+04 2.18772e-06</div><div><br></div><div>DD step 4 load imb.: force 181.0%</div></div><div><br></div><div>Not all bonded interactions have been properly assigned to the domain decomposition cells</div>
<div><br></div><div>A list of missing interactions:</div><div> Angle of 1001 missing -158</div><div> Ryckaert-Bell. of 910 missing -211</div><div> LJ-14 of 910 missing -270</div>
<div><br></div><div>Molecule type 'Protein'</div><div>the first 10 missing interactions, except for exclusions:</div><div> Ryckaert-Bell. atoms 279 280 281 282 global 279 280 281 282</div><div> Ryckaert-Bell. atoms 303 304 305 306 global 303 304 305 306</div>
<div> Angle atoms 304 305 306 global 304 305 306</div><div> Ryckaert-Bell. atoms 304 305 306 307 global 304 305 306 307</div><div> Ryckaert-Bell. atoms 316 317 318 319 global 316 317 318 319</div>
<div> Angle atoms 317 318 319 global 317 318 319</div><div> Ryckaert-Bell. atoms 317 318 319 320 global 317 318 319 320</div><div> Ryckaert-Bell. atoms 344 345 346 347 global 344 345 346 347</div>
<div> Ryckaert-Bell. atoms 485 486 487 488 global 485 486 487 488</div><div> Angle atoms 486 487 488 global 486 487 488</div><div><br></div><div>-------------------------------------------------------</div>
<div>Program mdrun, VERSION 4.5.4</div><div>Source code file: domdec_top.c, line: 352</div><div><br></div><div>Software inconsistency error:</div><div>One or more interactions were multiple assigned in the domain decompostion</div>
<div>For more information and tips for troubleshooting, please check the GROMACS</div><div>website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a></div><div>-------------------------------------------------------</div>
<div><br></div><div><br></div><div><br></div><div>I am having trouble tracking down the source of the error - the documentation on this sort of thing is sparse.</div><div><br></div><div>Thanks so much in advance,</div><div>
<br></div><br clear="all"><div><br></div>-- <br><div>Olivia Waring </div>
<div>Princeton University '12</div>
<div>AB Chemistry</div><br>
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