Dear Gerrit,
After trying a few different settings of .mdp, I found that "cutoff-scheme = Verlet" and "QMMMscheme = ONIOM" were causing the error. Would you have any idea how were these two settings linked to the generation of ".pc" file, and what would you suggest if I have to run under ONIOM? Thank you. Best regards, Zoe ________________________________ From: CHAN, Zoe ZC [Student] <zoe.zc.c...@connect.polyu.hk> Sent: 27 November 2017 18:23 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] QM/MM-ORCA Point Charge Correction Error (Zoe Chan) Dear Gerrit, Thank you very much for your prompt reply. I’ve tried to run the simulation with wenjin’s tutorial and it passed the point charge correction step with no problem. I compared the “.out” output files of my protein and of the tutorial peptide, I noticed there’s a line “%pointcharges “peptide.pc”” at the end of the input file section, I guess it shows that the basename has been linked to the “.pc” point charge file instead of the default name “temp.pc”, and it’s missing in my protein’s output file. Would that have possibly caused the crash? Again, thank you for your help. Best regards, Zoe On 27 Nov 2017, at 6:11 PM, Groenhof, Gerrit <ggro...@gwdg.de<mailto:ggro...@gwdg.de>> wrote: >From the error message it seems that ORCA program crashes. Unfortunately, Orca >is no longer supported, which means that if the ORCA's input or anything else >has changed, the gromacs interface may fail. What you could try is to use the version of ORCA that others have used before. Best, Gerrit Content-Type: text/plain; charset="iso-8859-1" Dear Gromacs Users, I've been running a QM/MM calculation on a protein with fluorescence probe, using gromacs 4.6.7 (double precision with MPI) and ORCA 4.0.1. The following lines were included in the .mdp file, QMMM = yes QMMM-grps = QMatoms QMmethod = B3LYP QMbasis = 6-31G* QMMMscheme = ONIOM QMcharge = -2 QMmult = 2 The run was aborted with the error messages, FATAL ERROR ENCOUNTERED CANNOT OPEN FILE Filename: temp.pc *** Process received signal *** Signal: Segmentation fault (11) Signal code: Address not mapped (1) Failing at address: (nil) [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x11390)[0x2ba5c5ada390] [ 1] /lib/x86_64-linux-gnu/libc.so.6(fgets+0x1e)[0x2ba5c5d53aee] [ 2] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(read_orca_output+0x1d8)[0x2ba5c4959b98] [ 3] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(call_orca+0xf0)[0x2ba5c495a0d0] [ 4] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(calculate_QMMM+0xa67)[0x2ba5c496a647] [ 5] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(do_force_lowlevel+0x1629)[0x2ba5c487cdf9] [ 6] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(do_force_cutsVERLET+0x17bb)[0x2ba5c48cc31b] [ 7] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(do_force+0x17f)[0x2ba5c48d02ef] [ 8] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(do_steep+0x5b3)[0x2ba5c48e4c33] [ 9] mdrun_mpi_d(mdrunner+0x15f2)[0x40f172] [10] mdrun_mpi_d(cmain+0x1a17)[0x433f67] [11] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x2ba5c5d06830] [12] mdrun_mpi_d(_start+0x29)[0x4072b9] *** End of error message *** Segmentation fault (core dumped) I am clueless on where the error came from, would anyone have any insight? Thank you. Best regards, Zoe [http://mlm.polyu.edu.hk/PolyU80_Email_Signature.png] www.polyu.edu.hk/80anniversary<http://www.polyu.edu.hk/80anniversary><http://www.polyu.edu.hk/80anniversary> Disclaimer: This message (including any attachments) contains confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this message and notify the sender and The Hong Kong Polytechnic University (the University) immediately. Any disclosure, copying, or distribution of this message, or the taking of any action based on it, is strictly prohibited and may be unlawful. The University specifically denies any responsibility for the accuracy or quality of information obtained through University E-mail Facilities. Any views and opinions expressed are only those of the author(s) and do not necessarily represent those of the University and the University accepts no liability whatsoever for any losses or damages incurred or caused to any party as a result of the use of such information. ------------------------------ -- 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<mailto:gmx-users-requ...@gromacs.org>. [http://mlm.polyu.edu.hk/PolyU80_Email_Signature.png] www.polyu.edu.hk/80anniversary<http://www.polyu.edu.hk/80anniversary> Disclaimer: This message (including any attachments) contains confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this message and notify the sender and The Hong Kong Polytechnic University (the University) immediately. Any disclosure, copying, or distribution of this message, or the taking of any action based on it, is strictly prohibited and may be unlawful. The University specifically denies any responsibility for the accuracy or quality of information obtained through University E-mail Facilities. Any views and opinions expressed are only those of the author(s) and do not necessarily represent those of the University and the University accepts no liability whatsoever for any losses or damages incurred or caused to any party as a result of the use of such information. [http://mlm.polyu.edu.hk/PolyU80_Email_Signature.png] www.polyu.edu.hk/80anniversary<http://www.polyu.edu.hk/80anniversary> Disclaimer: This message (including any attachments) contains confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this message and notify the sender and The Hong Kong Polytechnic University (the University) immediately. Any disclosure, copying, or distribution of this message, or the taking of any action based on it, is strictly prohibited and may be unlawful. The University specifically denies any responsibility for the accuracy or quality of information obtained through University E-mail Facilities. Any views and opinions expressed are only those of the author(s) and do not necessarily represent those of the University and the University accepts no liability whatsoever for any losses or damages incurred or caused to any party as a result of the use of such information. -- 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.
