Hi Justin, Really appreciate your help. I have solved the problem following your suggestion :) I love this community~
2012/3/7 Justin A. Lemkul <[email protected]> > > > ming ma wrote: > >> Hi, >> >> 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. >> 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. >> >> Below is my mdp file, >> >> ; energy minimization >> integrator = l-bfgs >> nsteps = 5000 >> constraints = none >> emtol = 1.0 >> nstcgsteep = 10 ; do a steep every 10 steps of cg >> emstep = 0.01 ; used with steep >> nbfgscorr = 10 >> nstcomm = 0 ; frequecy of remove of com movement >> Tcoupl = no >> Pcoupl = no >> >> ; potential and neigbor related >> coulombtype = Cut-off >> rcoulomb = 1.2 >> vdw-type = Switch >> rvdw-switch = 0.8 >> rvdw = 1.0 >> ; neighbor list related >> rlist = 1.2 >> nstlist = 10 >> ns_type = grid >> >> pbc = xyz >> ;output section >> nstxout = 0 >> nstvout = 0 >> nstfout = 0 >> nstlog = 100 >> nstenergy = 100 >> nstxtcout = 0 >> xtc_precision = 1000 >> xtc-grps = >> energygrps = >> >> And these are parts of the message I got during simulation, >> >> There were 262 inconsistent shifts. Check your topology >> Will stop reporting inconsistent shifts >> >> This is the results I got >> Low-Memory BFGS Minimizer converged to Fmax < 1 in 432 steps >> Potential Energy = 1.85767014488657e+05 >> >> I also tried using the cg method instead of l-bfgs, after read the log >> files carefully, I found these messages, >> >> Initializing Domain Decomposition on 4 nodes >> Dynamic load balancing: no >> Will sort the charge groups at every domain (re)decomposition >> Initial maximum inter charge-group distances: >> two-body bonded interactions: 14.880 nm, Morse, atoms 8401 8540 >> multi-body bonded interactions: 20.914 nm, G96Angle, atoms 8470 8540 >> Minimum cell size due to bonded interactions: 23.006 nm >> >> 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. >> >> > Exactly, the periodicity is not being handled correctly. Presumably > you're dealing with an infinite sheet (thus bonds extend across periodic > boundaries), and thus you need to set "periodic_molecules = yes" in the > .mdp file. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Dr. Ming MA Department of Chemistry, University College London London Centre for Nanotechnology 17-19 Gordon Street London WC1H 0AH
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