Does this also happen if you use pbc? gerrit On 10 Dec 2011, at 10:59, gmx-users-requ...@gromacs.org wrote:
> Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. qm/mm(orca/gromacs) (li yan) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 10 Dec 2011 17:59:11 +0800 > From: li yan <yanbochen...@gmail.com> > Subject: [gmx-users] qm/mm(orca/gromacs) > To: gmx-users@gromacs.org > Message-ID: > <caasmsb+swoenh3o6vrvo_hjbw_mtqjo2w0vdjk4hso3bbdo...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Gromacs developers: > > I'm trying to run a QM-MM single point energy calculation on a > structure (a small molecule with 50 water molecules with no pbc, no > cutoff). I use orca for QM part amd gromacs for MM part. But when I > run mdrun -nt 1 -s sp.tpr -c sp.gro -g sp.log, the ORCA run quickly > and terminate naormally, but after that mdrun run stops with a > segmentation fault. Here is the error information: > > Back Off! I just backed up sp.log to ./#sp.log.1# > > Reading file sp.tpr, VERSION 4.5.5 (single precision) > > QM/MM calculation requested. > > there we go! > > Layer 0 > > nr of QM atoms 9 > > QMlevel: MP2/3-21G > > /home/user/orca_x86_64_exe_r2360/home/user/programs/orca_x86_64_exe_r2360... > > orca initialised... > > Back Off! I just backed up traj.trr to ./#traj.trr.1# > > Back Off! I just backed up ener.edr to ./#ener.edr.1# > > starting mdrun 'Protein' > > 0 steps, 0.0 ps. > > Calling '/home/li/programs/orca_x86_64_exe_r2360/orca > /home/li/Test/test_gmx/qmmm/test/sp.inp >> > /home/li/Test/test_gmx/qmmm/test/sp.out' > > Segmentation fault > > Here is my sp.mdp > > title = test > > cpp =/lib/cpp > > integrator = md > > nsteps = 0 > > dt = 0.001 > > ;constraints = none > > emtol = 10.0 > > emstep = 0.01 > > nstcomm = 1 > > ns-type = simple > > nstlist = 0 > > rlist = 0 > > rcoulomb = 0 > > rvdw = 0 > > tcoupl = no > > pcoupl = no > > gen-vel = no > > nstxout = 1 > > nstlog = 1 > > nstenergy = 1 > > nstvout = 1 > > nstfout = 1 > > pbc = no > > comm_mode = angular > > ; non-equilibrium md > > freezegrps = System > > freezedim = y y y > > xtc_grps = System > > energygrps = System > > ;qmmm calculation > > QMMM = yes > > QMMM-grps = QMatoms > > QMMMscheme = normal > > QMmethod = MP2 > > QMbasis = 3-21g > > QMcharge = 0 > > QMmult = 1 > > The *.ORCAINFO is: > > ! RKS b3lyp/g sv(p) tightscf > > And I also tried QMMMsheme=ONIOM, but I get the segmentation fault > too. Am I missing something in all of this? > or the orca/gromcas can not be used to non periodic system? > Any help would be highly appreciated. > > Thanks > > Yan > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20111210/0755a046/attachment.html > > ------------------------------ > > -- > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 92, Issue 56 > ***************************************** -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
