Dear Justin, Thank you for your quick answer.
Same with GROMACS-4.6.6: core-to-shell distance must be >0 to not crash. My crystal is expected to be polarized (metallic and oxygen sites are the victims of this model). The *.mpd file being used is: # nstcalcenergy = 1 ; 4.6.6 claims this necessary, 4.6.3 didn't need it # integrator = steep # vdw-type = cut-off # coulombtype = pme # nsteps = 10 # periodic-molecules = no # cutoff-scheme = group # ns-type = grid # emtol = 10 ; default=10 kJ/mol/nm # niter = 10000 ; default=20 # ;fcstep = ; default=0 ps^2 ; not quite clear what it is # rlist = 1.0 # rcoulomb = 1.0 # rvdw = 1.0 # pbc = xyz # nstxout = 1 ; wouldn't emit pos for each, though # nstfout = 1 ; -"- # nstlist = 1000 ; avoid it, no bonds at all # nstlog = 1 # ;pcoupl = no ; used to switch cell-optimization on/off Best regards, toma On Fri, Jul 25, 2014 at 1:48 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/25/14, 7:43 AM, Tamas Karpati wrote: >> >> Dear all, >> >> I have two questions about geometry optimization of a crystal >> with polarization via the core/shell model. I'm creating *.gro and >> *.top files "by hand" and compile them with *.mdp to *.tpr via >> GROMPP. My FF is also made by hand (simply because i need >> to learn GROMACS). I have learnt on this list that with Buckingham >> potentials I need to use the group rather than the Verlet scheme. >> >> >> (1/2) Letting some of all atoms be polarizable through applying >> shell particles made MDRUN segfault like this: >> >> # ... >> # Reading file AAA_opt.tpr, VERSION 4.6.3 (single precision) >> # Using 2 MPI threads >> # >> # Steepest Descents: >> # Tolerance (Fmax) = 1.00000e+01 >> # Number of steps = 10 >> # Segmentation fault1.0e-02 nm, Epot= -nan Fmax= 3.76506e+03, >> atom= 1357 >> >> I imagined some divison by zero situation not handled and have put >> some "random noise" on the shell particles' position so they do not >> anymore start exactly at the atomic sites (meaning nonzero distances). >> Seemed to work, at least no further crashes. Only energies and forces >> seem very high: >> >> # Steepest Descents: >> # Tolerance (Fmax) = 1.00000e+01 >> # Number of steps = 10 >> # Step= 0, Dmax= 1.0e-02 nm, Epot= -1.36425e+07 Fmax= 2.99600e+05, >> atom= 160 >> # Step= 1, Dmax= 1.0e-02 nm, Epot= -1.62080e+07 Fmax= 1.25769e+06, >> atom= 160 >> # Step= 2, Dmax= 1.2e-02 nm, Epot= -1.95965e+07 Fmax= 6.87820e+08, >> atom= 2759 >> # Step= 3, Dmax= 1.4e-02 nm, Epot= -2.02902e+07 Fmax= 1.30719e+09, >> atom= 468 >> # Step= 8, Dmax= 1.1e-03 nm, Epot= -2.18970e+07 Fmax= 5.77722e+09, >> atom= 1095 >> # Step= 10, Dmax= 6.5e-04 nm, Epot= -1.96952e+07 Fmax= 3.92889e+08, >> atom= 1096 >> # Energy minimization reached the maximum numberof steps before the >> forces >> # reached the requestedprecision Fmax < 10. >> >> My question is the following. >> Is it (randomized shell positions) a correct procedure with GROMACS? >> >> >> (2/2) Changing from a randomized x/y/z set to a fixed distance at >> a random direction for the shell particles led to another unexpected >> result. >> I scanned a range between 1e-4 to 0.1 nm and noticed that >> >> the final core-to-shell distance is a function of the starting one. >> >> I used niter = 10000 (note: the default is 20) as i noticed in an MD >> type of job that 20, 100 or 1000 steps were insufficient for the shells >> to relax within default tolerance. The cell size was ca. 3x3x3 nm. >> > > Please provide a full .mdp file; other settings are very relevant. > > >> My question is the following. >> What would be the appropriate core-to-shell distance to apply? >> > > The equilibrium distance for core-shell bonds should be zero, deviations > from this non-polarized state account for the polarization energy. > > >> I appreciate any help so thanks in advance. > > > Upgrade to 4.6.6; there have been issues with shells that have been fixed > since 4.6.3. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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