Dear Gromacs users! I'm trying to interface gromacs (5.0) with orca (2.9.1), although i encountered some problems. I'm testing a tripeptide system which i found here: http://www.picb.ac.cn/~liwenjin/QMMM_simulations/index.html , but i'm using a different .mdp file, with these parameters (i copied the only working configuration): integrator = steep dt = 0.002 ; ps ! nsteps = 10000 nstlist = 10 ns_type = grid rlist = 3.0 rcoulomb = 3.0 coulombtype = cut-off vdwtype = cut-off rvdw = 3.0 pbc = no periodic_molecules = no constraints = none energygrps = QMatoms MMatoms cutoff-scheme = group
; QM/MM calculation stuff QMMM = yes QMMM-grps = QMatoms QMmethod = rhf QMbasis = 3-21G QMMMscheme = normal QMcharge = 0 QMmult = 1 bOPT = no bTS = no SH = no ; ; Energy minimizing stuff ; emtol = 60 ; minimization thresold (kj/mol.nm-1) 1 hartree/bohr= 49614.75241 kj/mol.nm-1 1 kj/mol.nm-1=2.01553e-5 hartree/bohr emstep = 0.01 ; minimization step in nm with the .ORCAINFO file of ! LDA cc-(p)VDZ %LJcoefficients "peptide.LJ" %pointcharges "peptide.pc" %geom end After i modified the ffnonbonded.itp and atomtypes.atp for the dummy atom, rebuilt the gromacs and the grompp and mdrun commands were executed with the following: grompp -p peptide.top -c peptide.gro -f peptide.mdp -n peptide.ndx -o peptide.tpr mdrun -s peptide.tpr -c peptide.gro -o peptide.trr -e peptide.edr -g peptide.log The first thing is, that the default neighbor searching algorithm - cutoff-scheme=verlet - isn't producing any point charges for ORCA and the job ends with a segmentation fault, although the group cutoff scheme works well. It is not clear to me why this is happening, but i suspect the problem lies in that the qm/mm subrutines are quite old (~2003?), and the verlet scheme introduced much later in gromacs 4.6 (2013). The second problem that i have encountered is with the pbc options: if i'm using pbc=xyz the job terminates with a segmentation fault (core dumped) after orca terminates normally. After i looked for some explanation about coordinate updating on the qmmm.c source file I saw some comments that the update_QMMMrec function not working properly without pbc, even though it works just fine with pbc=no. Little bit confused of that, although the gromacs was tested on the regression package and all the tests passed. The third problem is with the bOPT = yes option. When i pass the optimization to the orca, after the first optimization cycle (before orca terminates normally) the tripeptide's qm region forms an unrealistic geometry. At the input of the second orca run, the qm region scatters, the atoms move apart around 10 angströms from each other and gives the following error message: Error (ORCA_GSTEP): The lambda equations have not converged although, the job continues and at the third orca run gives the following: Calling '/export/home/hegely/Programz/orca_2_9_1_linux_x86-64/orca peptide.inp >> peptide.out' !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!! FATAL ERROR ENCOUNTERED !!! !!! ----------------------- !!! !!! I/O OPERATION FAILED !!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ABORTING THE RUN and the job runs onward, giving the same error message over and over until i kill it. In the gromacs .log file no error messages are presented and i don't really have a clue of what's going on. Maybe the point charges destroy the geometry of the peptide? I think i checked all the qm/mm, orca searching results in the gmx-users list, but didn't find the solutions. Sorry if i missed something out, but i would appreciate any help! Bence Hégely -- 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.