<br><br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">sreelakshmi ramesh</b> <span dir="ltr"><<a href="mailto:sree.lakshmi@research.iiit.ac.in">sree.lakshmi@research.iiit.ac.in</a>></span><br>
Date: Sat, Jun 11, 2011 at 4:37 PM<br>Subject: Re: error during equilibriation<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br><br><br><pre>here goes my mdp file.The when i attach the top file by mail is getting bounced back.Thanks in adcvance <br>
<br><br><br>title = double walled cnt between graphene sheets<br>define = -DPOSRES position restrain the protein<br>; Run parameters<br>
integrator = md leap-frog integrator<br>nsteps = 50000 2 * 50000 = 100 ps<br>dt = 0.002 2 fs<br>; Output control<br>nstxout = 100 save coordinates every 0.2 ps<br>nstvout = 100 save velocities every 0.2 ps<br>
nstenergy = 100 save energies every 0.2 ps<br>nstlog = 100 update log file every 0.2 ps<br>; Bond parameters<br>continuation = no first dynamics run<br>constraint_algorithm = lincs holonomic constraints <br>constraints = all-bonds all bonds (even heavy atom-H bonds) constrained<br>
lincs_iter = 1 accuracy of LINCS<br>lincs_order = 4 also related to accuracy<br>; Neighborsearching<br>ns_type = grid search neighboring grid cells<br>nstlist = 5 10 fs<br>rlist = 1.0 short-range neighborlist cutoff (in nm)<br>
rcoulomb = 1.0 short-range electrostatic cutoff (in nm)<br>rvdw = 1.0 short-range van der Waals cutoff (in nm)<br>; Electrostatics<br>coulombtype = PME Particle Mesh Ewald for long-range electrostatics<br>pme_order = 4 cubic interpolation<br>
fourierspacing = 0.16 grid spacing for FFT<br>; Temperature coupling is on<br>tcoupl = V-rescale modified Berendsen thermostat<br>tc-grps = system two coupling groups - more accurate<br>tau_t = 0.1 time constant, in ps<br>
ref_t = 300 reference temperature, one for each group, in K<br>; Pressure coupling is off<br>pcoupl = no no pressure coupling in NVT<br>; Periodic boundary conditions<br>pbc = xyz 3-D PBC<br>; Dispersion correction<br>
DispCorr = EnerPres account for cut-off vdW scheme<br>; Velocity generation<br>gen_vel = yes assign velocities from Maxwell distribution<br>gen_temp = 300 temperature for Maxwell distribution<br>gen_seed = -1 generate a random seed<br>
<br><br>here goes the error<br>Not all bonded interactions have been properly assigned to the domain decomposition cells<div class="im"><br><br>A list of missing interactions:<br> Angle of 2097 missing 14<br>
Ryckaert-Bell. of 1286 missing 12<br>
LJ-14 of 2801 missing 8<br> exclusions of 31870 missing 14<br><br>Molecule type 'ICE'<br>the first 10 missing interactions, except for exclusions:<br> LJ-14 atoms 79 299 global 79 299<br>
LJ-14 atoms 165 299 global 165 299<br> Angle atoms 167 207 299 global 167 207 299<br> Ryckaert-Bell. atoms 167 207 299 285 global 167 207 299 285<br>
Ryckaert-Bell. atoms 173 175 285 299 global 173 175 285 299<br> LJ-14 atoms 173 299 global 173 299<br> LJ-14 atoms 173 352 global 173 352<br> Angle atoms 175 285 299 global 175 285 299<br>
Angle atoms 175 285 352 global 175 285 352<br> Ryckaert-Bell. atoms 175 285 299 207 global 175 285 299 207<br><br>-------------------------------------------------------<br>Program mdrun, VERSION 4.5.3<br>
Source code file: domdec_top.c, line: 356<br><br>Fatal error:<br>48 of the 46602 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1 nm) or the two-body cut-off distance (1 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck<br>
For more information and tips for troubleshooting, please check the GROMACS<br>website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br><br></div>
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