Re: [gmx-users] what is MPI process rank 0 (n0, p18041) caught a SIGSEGV
Recompile the mopac library with larger arrays. You can set these in the SIZES file in the mopac sourcedir (MAXORB). Do not forget to recompile also mdrun afterwards,as the library (.a) will be statically linked. Gerrit Mahnam wrote: In God We Trust Hello GMX users I want to do QM/MM by Gromacs and mopac7.I installed Gromacs and mopac7.I am using ffoplsaa. grompp make tpr ,but when I run mdrun it says: Back Off! I just backed up a.log to ./#a.log.5# Reading file a4.tpr, VERSION 3.3 (single precision) QM/MM calculation requested. Layer 0 nr of QM atoms 147 QMlevel: PM3/STO-3G MAXIMUM NUMBER OF ATOMIC ORBITALS EXCEEDED MAXIMUM ALLOWED = 200 keywords are: PRECISE GEO-OK CHARGE=0 GRAD MMOK ANALYT PM3 Back Off! I just backed up a.edr to ./#a.edr.5# Steepest Descents: Tolerance (Fmax) = 1.0e+02 Number of steps= 1000 counting the number of NH-C=O groups *MPI process rank 0 (n0, p18041) caught a SIGSEGV*. and here is the end of my md.log file Initializing LINear Constraint Solver number of constraints is 6 average number of constraints coupled to one constraint is 0.0 Steepest Descents: Tolerance (Fmax) = 1.0e+02 Number of steps= 1000 Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.098311 1707 1710 0.093123 After LINCS 0.03 1684 1687 0.01 Going to use C-settle (1267 waters) wo = 0.33, wh =0.33, wohh = 3, rc = 0.08165, ra = 0.0384897 rb = 0.0192449, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1 Grid: 9 x 9 x 6 cells Configuring nonbonded kernels... Testing AMD 3DNow support... not present. Testing ia32 SSE support... present. I do not have any idea why this is happening?.May I ask you what does it means? Any help will be greatly appreciated Karim Mahnam Institute of Biochemistry and Biophysics (IBB) Tehran University P.O.box 13145-1384 Tehran Iran http://www.ibb.ut.ac.ir/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php
[gmx-users] what is MPI process rank 0 (n0, p18041) caught a SIGSEGV
In God We TrustHello GMX users I want to do QM/MM by Gromacs and mopac7.I installed Gromacsand mopac7.I am using ffoplsaa. grompp make tpr ,but when I run mdrun it says: Back Off! I just backed up a.log to ./#a.log.5#Reading file a4.tpr, VERSION 3.3 (single precision)QM/MM calculation requested.Layer 0 nr of QM atoms 147QMlevel: PM3/STO-3G MAXIMUM NUMBER OF ATOMIC ORBITALS EXCEEDED MAXIMUM ALLOWED = 200keywords are: PRECISE GEO-OK CHARGE=0 GRAD MMOK ANALYT PM3 Back Off! I just backed up a.edr to ./#a.edr.5#Steepest Descents: Tolerance (Fmax) = 1.0e+02 Number of steps = 1000counting the number of NH-C=O groupsMPI process rank 0 (n0, p18041) caught a SIGSEGV. and here is the end of my md.log file Initializing LINear Constraint Solver number of constraints is 6 average number of constraints coupled to one constraint is 0.0 Steepest Descents: Tolerance (Fmax) = 1.0e+02 Number of steps = 1000 Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.098311 1707 1710 0.093123 After LINCS 0.03 1684 1687 0.01 Going to use C-settle (1267 waters)wo = 0.33, wh =0.33, wohh = 3, rc = 0.08165, ra = 0.0384897rb = 0.0192449, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1Grid: 9 x 9 x 6 cellsConfiguring nonbonded kernels...Testing AMD 3DNow support... not present.Testing ia32 SSE support... present. I do not have any idea why this is happening?.May I ask you what does it means?Any help will be greatly appreciatedKarim MahnamInstitute of Biochemistry and Biophysics (IBB)Tehran University P.O.box 13145-1384Tehran Iran http://www.ibb.ut.ac.ir/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php
[gmx-users] what is MPI process rank 0 (n0, p18041) caught a SIGSEGV ?
In God We TrustHello GMX users I want to do QM/MM by Gromacs and mopac7.I install Gromacsand mopac7.when I run mdrun it says: Back Off! I just backed up a.log to ./#a.log.5#Reading file a4.tpr, VERSION 3.3 (single precision)QM/MM calculation requested.Layer 0 nr of QM atoms 147QMlevel: PM3/STO-3G MAXIMUM NUMBER OF ATOMIC ORBITALS EXCEEDED MAXIMUM ALLOWED = 200keywords are: PRECISE GEO-OK CHARGE=0 GRAD MMOK ANALYT PM3 Back Off! I just backed up a.edr to ./#a.edr.5#Steepest Descents: Tolerance (Fmax) = 1.0e+02 Number of steps = 1000counting the number of NH-C=O groupsMPI process rank 0 (n0, p18041) caught a SIGSEGV. and here is the end of my md.log file Initializing LINear Constraint Solver number of constraints is 6 average number of constraints coupled to one constraint is 0.0 Steepest Descents: Tolerance (Fmax) = 1.0e+02 Number of steps = 1000 Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.098311 1707 1710 0.093123 After LINCS 0.03 1684 1687 0.01 Going to use C-settle (1267 waters)wo = 0.33, wh =0.33, wohh = 3, rc = 0.08165, ra = 0.0384897rb = 0.0192449, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1Grid: 9 x 9 x 6 cellsConfiguring nonbonded kernels...Testing AMD 3DNow support... not present.Testing ia32 SSE support... present. I do not have any idea why this is happening?.May I ask you what does it means?Any help will be greatly appreciatedKarim MahnamInstitute of Biochemistry and Biophysics (IBB)Tehran University P.O.box 13145-1384Tehran Iran http://www.ibb.ut.ac.ir/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php
