Hi,<br><br>Thanks for looking at this email. Before I asked this question, I have read most of the related topics in gromacs's mailing list, but still can't solve it.<br>When I was trying to do energy minimization of graphene with pbc, I got several messages "there are # inconsistent shifts, check your topolgy." After the mimization is finished, the energy in extremely large (1.86e+05 kJ/mol), which is obviously wrong. To make sure that I haven't done any stupid mistake, I have carried out energy minimization of the same system using LAMMPS, and the results is reasonable (the energy is -205.14 eV). The configuration of the system has also been checked by visualizing it in VMD, and the PBC seems right.<br>
<br>Below is my mdp file,<br><br>; energy minimization<br>integrator = l-bfgs<br>nsteps = 5000<br>constraints = none<br>emtol = 1.0<br>nstcgsteep = 10 ; do a steep every 10 steps of cg<br>
emstep = 0.01 ; used with steep<br>nbfgscorr = 10<br>nstcomm = 0 ; frequecy of remove of com movement<br>Tcoupl = no<br>Pcoupl = no<br>
<br>; potential and neigbor related<br>coulombtype = Cut-off<br>rcoulomb = 1.2<br>vdw-type = Switch<br>rvdw-switch = 0.8<br>rvdw = 1.0<br>; neighbor list related<br>
rlist = 1.2<br>nstlist = 10<br>ns_type = grid<br><br>pbc = xyz<br>;output section<br>nstxout = 0<br>nstvout = 0<br>
nstfout = 0<br>nstlog = 100<br>nstenergy = 100<br>nstxtcout = 0<br>xtc_precision = 1000<br>xtc-grps =<br>energygrps =<br>
<br>And these are parts of the message I got during simulation,<br><br>There were 262 inconsistent shifts. Check your topology<br>Will stop reporting inconsistent shifts<br><br>This is the results I got<br>Low-Memory BFGS Minimizer converged to Fmax < 1 in 432 steps<br>
Potential Energy = 1.85767014488657e+05<br><br>I also tried using the cg method instead of l-bfgs, after read the log files carefully, I found these messages,<br><br>Initializing Domain Decomposition on 4 nodes<br>Dynamic load balancing: no<br>
Will sort the charge groups at every domain (re)decomposition<br>Initial maximum inter charge-group distances:<br> two-body bonded interactions: 14.880 nm, Morse, atoms 8401 8540<br> multi-body bonded interactions: 20.914 nm, G96Angle, atoms 8470 8540<br>
Minimum cell size due to bonded interactions: 23.006 nm<br><br clear="all">I checked the distances between the atoms it showed, obviously, this large distance is caused by not having taken the pbc xyz into consideration since the size of the simulation box is 15*15**6 nm. So does it mean I haven't handle the pbc correctly? Since I notice in the message posted before some of the 'inconsistent shifts' are also caused by pbc problems.<br>
<br>Thanks for your kind help<br> <br>-- <br>Dr. Ming MA<br>Department of Chemistry, University College London<div>London Centre for Nanotechnology<div><span style="font-size:13px;font-family:arial,sans-serif">17-19 Gordon Street<br>
London<br>WC1H 0AH</span><br></div></div><br>