Re: [gmx-users] QMMM
I did follow the Gaussian/Gromacs QM/MM set up guide too and was not successful. On Tue, Mar 8, 2011 at 1:28 PM, Jack Shultz jackygraha...@gmail.com wrote: Good luck. I followed the instructions and was not successful. On Tue, Mar 8, 2011 at 12:48 AM, Haresh ajanihar...@gmail.com wrote: Hello everyone, I want install gromacs with mopac7 for qmmm. Can you guide me for installation procedure Thank you. -- 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 -- 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 -- gmx-users mailing listgmx-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
Re: [gmx-users] GAUSSIAN Error message
# HF/6-31G OPT FREQ ^M ^M ARGUSLAB-GENERAT Could be related to the ^M ^M characters? This sometimes happens when you transfer files form windows to linux. You may try dos2unix On Thu, Feb 24, 2011 at 8:07 PM, Sergio Manzetti sergio.manze...@vestforsk.no wrote: No. It contains a charged Gandolinium ion in the middle of a buckyball. On Fri, Feb 25, 2011 at 2:59 AM, TJ Mustard musta...@onid.orst.edu wrote: On February 24, 2011 at 10:29 AM Sergio Manzetti sergio.manze...@vestforsk.no wrote: Hello, I am getting an unknown error message in the submission of the G03 file: QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE. # HF/6-31G OPT FREQ ^M ^M ARGUSLAB-GENERAT ' Last state=GCL TCursr= 909 LCursr= 20 Error termination via Lnk1e in Gaussian64/g03/l1.exe at Thu Feb 24 19:26:31 2011. Job cpu time: 0 days 0 hours 0 minutes 0.1 seconds. File lengths (MBytes): RWF= 9 Int= 0 D2E= 0 Chk= 1 Scr= 1 The submission file is prepared in Argus Lab and looks as follows: %chk=BuckyBall.chk # HF/6-31G Opt Freq ArgusLab-generated input file for BuckyBall 0 3 You have a no charge triplet? Is this a carbene? TJ Mustard C -0.677394 -0.928398 -3.166238 C 0.672998 -0.928446 -3.166308 C 1.090287 0.355662 -3.166349 C -0.002252 1.149252 -3.166236 C -1.094761 0.355692 -3.166308 C -2.207300 0.717126 -2.443529 C -1.364869 -1.874482 -2.443334 C 1.360544 -1.874612 -2.443455 C 2.202769 0.717064 -2.443539 C -0.002273 2.318671 -2.443310 C 2.453119 -1.519766 -1.733636 C 2.878066 -0.212169 -1.733664 C 2.202696 1.865587 -1.733573 C 1.090185 2.673574 -1.733478 C -1.094750 2.673602 -1.733477 C -2.207294 1.865663 -1.733587 C -2.882593 -0.212075 -1.733651 C -2.457472 -1.519622 -1.733552 C -0.689644 -2.803573 -1.733436 C 0.685341 -2.803673 -1.733490 C -1.364814 -3.022879 -0.584899 C -2.457440 -2.229447 -0.584919 C 1.360538 -3.023080 -0.584938 C 2.453142 -2.229641 -0.584965 C 3.295442 0.362133 -0.584991 C 2.877991 1.646286 -0.584972 C 0.672881 3.247762 -0.584900 C -0.677441 3.247772 -0.584900 C -2.882669 1.646412 -0.584987 C -3.300125 0.362235 -0.584997 C -0.677324 -3.246244 0.584596 C 0.673012 -3.246356 0.584600 C 2.878165 -1.644929 0.584675 C 3.295525 -0.360730 0.584685 C 2.453028 2.231040 0.584637 C 1.360422 3.024522 0.584617 C -2.457644 2.231133 0.584645 C -1.364978 3.024550 0.584620 C -2.882566 -1.644798 0.584681 C -3.300136 -0.360638 0.584699 C 1.090333 -2.672223 1.733208 C 2.202882 -1.864245 1.733311 C -2.207252 -1.864123 1.733266 C -1.094677 -2.672115 1.733166 C -2.882710 0.213674 1.733376 C -2.457667 1.521287 1.733309 C -0.689778 2.805232 1.733169 C 0.685256 2.805226 1.733176 C 2.878158 0.213598 1.733360 C 2.453109 1.521217 1.733301 C -0.002190 -2.317221 2.442969 C -2.207307 -0.715570 2.443173 C -1.364994 1.876105 2.443040 C 1.360490 1.876086 2.443059 C 2.202875 -0.715646 2.443217 C -0.677428 0.929925 3.165780 C 0.672958 0.929915 3.165806 C 1.090307 -0.354191 3.165883 C -0.002209 -1.147744 3.165767 C -1.094738 -0.354156 3.165831 Gd -0.004870 0.001706 -0.000166 --Link1-- %chk=BuckyBall.chk # HF/6-31G Opt Freq Cube=(orbitals) Geom=AllCheck Guess=(Read,Only) BuckyBall_orbitals.cub 212 213 --Link1-- %chk=BuckyBall.chk # HF/6-31G Opt Freq Cube=(density) Geom=AllCheck Guess=(Read,Only) BuckyBall_density.cub --Link1-- %chk=BuckyBall.chk # HF/6-31G Opt Freq Cube=(spin) Geom=AllCheck Guess=(Read,Only) BuckyBall_spin.cub --Link1-- %chk=BuckyBall.chk # HF/6-31G Opt Freq Cube=(potential) Geom=AllCheck Guess=(Read,Only) BuckyBall_potential.cub TJ Mustard Email: musta...@onid.orst.edu -- 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 -- 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.
Re: [gmx-users] Re: gromacs QM/MM compilation with gaussian (Txema Mercero)
On Wed, Feb 16, 2011 at 2:44 PM, Gerrit Groenhof ggro...@gwdg.de wrote: What is your path to the gaussian executable? GAUSS_EXE=/software/g03gromacs/g03 GAUSS_DIR=/software/g03gromacs/g03 In this directories are all gaussian l*.exe files. DEVEL_DIR=/software/g03gromacs/g03/modlinks Txema Gerrit On 16 Feb 2011, at 14:39, Txema Mercero wrote: I get the same error which I attach this time: - Back Off! I just backed up md.log to ./#md.log.8# Reading file topol.tpr, VERSION 4.5.3 (single precision) QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 24 QMlevel: RHF/6-31G number of CPUs for gaussian = 1 memory for gaussian = 5000 accuracy in l510 = 8 NOT using cp-mcscf in l1003 Level of SA at start = 0 /software/g03Gromacs/g03gaussian initialised... Back Off! I just backed up traj.trr to ./#traj.trr.3# Back Off! I just backed up ener.edr to ./#ener.edr.3# Steepest Descents: Tolerance (Fmax) = 1.0e+02 Number of steps = 1000 *** glibc detected *** /software/gromacs-4.5.3-shared-ifort11_gauss/bin/mdrun: malloc(): memory corruption: 0x077711b0 *** === Backtrace: = /lib64/libc.so.6[0x3ddcc724ac] /lib64/libc.so.6(__libc_calloc+0xc0)[0x3ddcc73ce0] /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libgmx.so.6(save_calloc+0x32)[0x2b0e5ba08462] /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libmd.so.6(call_gaussian+0x81)[0x2b0e5b38cfd1] /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libmd.so.6(call_QMroutine+0x25)[0x2b0e5b384265] /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libmd.so.6(calculate_QMMM+0x665)[0x2b0e5b383bb5] /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libmd.so.6(do_force_lowlevel+0xd9)[0x2b0e5b2fcbd9] /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libmd.so.6(do_force+0xdaf)[0x2b0e5b35ae6f] /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libmd.so.6(do_steep+0x7d6)[0x2b0e5b314a26] /software/gromacs-4.5.3-shared-ifort11_gauss/bin/mdrun[0x4149ba] /software/gromacs-4.5.3-shared-ifort11_gauss/bin/mdrun[0x41dc03] /lib64/libc.so.6(__libc_start_main+0xf4)[0x3ddcc1d974] /software/gromacs-4.5.3-shared-ifort11_gauss/bin/mdrun(do_nm+0x4f1)[0x407069] === Memory map: 0040-0046d000 r-xp 00:18 20054244 /software/gromacs-4.5.3-shared-ifort11_gauss/bin/mdrun 0066d000-00672000 rw-p 0006d000 00:18 20054244 /software/gromacs-4.5.3-shared-ifort11_gauss/bin/mdrun 00672000-00673000 rw-p 00672000 00:00 0 0770a000-077b6000 rw-p 0770a000 00:00 0 [heap] 3ddc80-3ddc81c000 r-xp 08:02 5751044 /lib64/ld-2.5.so 3ddca1b000-3ddca1c000 r--p 0001b000 08:02 5751044 /lib64/ld-2.5.so 3ddca1c000-3ddca1d000 rw-p 0001c000 08:02 5751044 /lib64/ld-2.5.so 3ddcc0-3ddcd4c000 r-xp 08:02 5750905 /lib64/libc-2.5.so 3ddcd4c000-3ddcf4c000 ---p 0014c000 08:02 5750905 /lib64/libc-2.5.so 3ddcf4c000-3ddcf5 r--p 0014c000 08:02 5750905 /lib64/libc-2.5.so 3ddcf5-3ddcf51000 rw-p 0015 08:02 5750905 /lib64/libc-2.5.so 3ddcf51000-3ddcf56000 rw-p 3ddcf51000 00:00 0 3ddd00-3ddd082000 r-xp 08:02 5750931 /lib64/libm-2.5.so 3ddd082000-3ddd281000 ---p 00082000 08:02 5750931 /lib64/libm-2.5.so 3ddd281000-3ddd282000 r--p 00081000 08:02 5750931 /lib64/libm-2.5.so 3ddd282000-3ddd283000 rw-p 00082000 08:02 5750931 /lib64/libm-2.5.so 3ddd40-3ddd402000 r-xp 08:02 5750939 /lib64/libdl-2.5.so 3ddd402000-3ddd602000 ---p 2000 08:02 5750939 /lib64/libdl-2.5.so 3ddd602000-3ddd603000 r--p 2000 08:02 5750939 /lib64/libdl-2.5.so 3ddd603000-3ddd604000 rw-p 3000 08:02 5750939 /lib64/libdl-2.5.so 3ddd80-3ddd816000 r-xp 08:02 5751046 /lib64/libpthread-2.5.so 3ddd816000-3ddda15000 ---p 00016000 08:02 5751046 /lib64/libpthread-2.5.so 3ddda15000-3ddda16000 r--p 00015000 08:02 5751046 /lib64/libpthread-2.5.so 3ddda16000-3ddda17000 rw-p 00016000 08:02 5751046 /lib64/libpthread-2.5.so 3ddda17000-3ddda1b000 rw-p 3ddda17000 00:00 0 3dddc0-3dddc14000 r-xp 08:02 10306767 /usr/lib64/libz.so.1.2.3 3dddc14000-3ddde13000 ---p 00014000 08:02 10306767 /usr/lib64/libz.so.1.2.3 3ddde13000-3ddde14000 rw-p 00013000 08:02 10306767 /usr/lib64/libz.so.1.2.3 3ddfc0-3ddfc15000 r-xp 08:02 5751016 /lib64/libnsl-2.5.so 3ddfc15000-3ddfe14000 ---p 00015000 08:02 5751016 /lib64/libnsl-2.5.so 3ddfe14000-3ddfe15000 r--p 00014000 08:02 5751016 /lib64/libnsl-2.5.so 3ddfe15000-3ddfe16000 rw-p 00015000 08:02 5751016 /lib64/libnsl-2.5.so 3ddfe16000-3ddfe18000 rw-p 3ddfe16000 00:00 0 3de440-3de4533000 r-xp 08:02 10310609 /usr/lib64/libxml2.so.2.6.26 3de4533000-3de4733000 ---p 00133000 08:02 10310609 /usr/lib64/libxml2.so.2.6.26 3de4733000-3de473c000 rw-p 00133000 08:02 10310609 /usr/lib64/libxml2.so.2.6.26 3de473c000-3de473d000 rw-p 3de473c000 00:00 0 3dea20-3dea20d000 r-xp 08:02 5751072
Re: [gmx-users] R. Re: Re: gromacs QM/MM compilation with gaussian (Txema Mercero) (Txema Mercero)
Here it goes. On Thu, Feb 17, 2011 at 9:49 AM, Gerrit Groenhof ggro...@gwdg.de wrote: 2. Re: Re: gromacs QM/MM compilation with gaussian (Txema Mercero) (Txema Mercero) Can you send me your tpr file? Gerrit -- 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 topol.tpr.gz Description: GNU Zip compressed data -- gmx-users mailing listgmx-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
Re: [gmx-users] R. Re: Re: gromacs QM/MM compilation with gaussian (Txema Mercero) (Txema Mercero)
Thanks Gerrit, Do you have any guess whether the problem could in in gromacs or Gaussian compilation? In the lines you sent me in your execution I see Calling '/home/ggroenh/g09//g09 input.com input.log But I do not see something like this in our exectution. By the way are there somewhere instruction for g09? Or I can just apply the changes mentioned in http://wwwuser.gwdg.de/~ggroenh/roadmap.pdf ? Thanks for your help. On Thu, Feb 17, 2011 at 10:52 AM, Gerrit Groenhof ggro...@gwdg.de wrote: Hi, With gmx 5.5.3 your input works here. Still it crashes in g09, but that is because you have a multiplicity of 1 with 181 electrons. QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 24 QMlevel: RHF/6-31G number of CPUs for gaussian = 1 memory for gaussian = 5000 accuracy in l510 = 8 NOT using cp-mcscf in l1003 Level of SA at start = 0 /home/ggroenh/g09/gaussian initialised... Steepest Descents: Tolerance (Fmax) = 1.0e+02 Number of steps = 1000 Calling '/home/ggroenh/g09//g09 input.com input.log' --- Program mdrun, VERSION 4.5.3 Source code file: qm_gaussian.c, line: 913 Fatal error: Call to '/home/ggroenh/g09//g09 input.com input.log' failed For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I Used To Care, But Things Have Changed (Bob Dylan) On 02/17/2011 10:39 AM, Txema Mercero wrote: Here it goes. On Thu, Feb 17, 2011 at 9:49 AM, Gerrit Groenhofggro...@gwdg.de wrote: 2. Re: Re: gromacs QM/MM compilation with gaussian (Txema Mercero) (Txema Mercero) Can you send me your tpr file? Gerrit -- 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 -- gmx-users mailing listgmx-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
[gmx-users] Re: gromacs QM/MM compilation with gaussian
Hi there! We are trying to compile gromacs with Gaussian 03 rev D.02 (we also have g09). We followed the instructions in http://wwwuser.gwdg.de/~ggroenh/roadmap.pdf despite that they do no fit exactly with the g03 rev d03 version,for instance, FrcNCN is no in l710 but in utilam.F Despite of that, we compiled gromacs and apparently everything was fine, but we get a segmentation fault when we run gromacs. We have the following questions 1.- Is it possible to get a more detailed/or specific instructions? 2.- I think that three variables GAUSS_EXE, GAUSS_DIR and DEVEL_DIR should be defined. Where should GAUSS_EXE and GAUSS_DIR point exactly? Thanks for your attention, any help will be appreciated. Regards, Txema Mercero IZO/SGI UPV/EHU -- gmx-users mailing listgmx-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
Re: [gmx-users] Re: gromacs QM/MM compilation with gaussian (Txema Mercero)
0007e000 00:18 20054237 /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libgmxpreprocess.so.6.0.0 2b0e5b27d000-2b0e5b28 rw-p 0007d000 00:18 20054237 /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libgmxpreprocess.so.6.0.0 2b0e5b28-2b0e5b2ae000 rw-p 2b0e5b28 00:00 0 2b0e5b2ae000-2b0e5b3b9000 r-xp 00:18 20054231 /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libmd.so.6.0.0 2b0e5b3b9000-2b0e5b5b9000 ---p 0010b000 00:18 20054231 /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libmd.so.6.0.0 2b0e5b5b9000-2b0e5b5bc000 rw-p 0010b000 00:18 20054231 /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libmd.so.6.0.0 2b0e5b5bc000-2b0e5b5bd000 rw-p 2b0e5b5bc000 00:00 0 2b0e5b5bd000-2b0e5b74c000 r-xp 00:18 49184804 /software/fftw-3.2.2_intel_11.0.069/lib/libfftw3f.so.3.2.4 2b0e5b74c000-2b0e5b94b000 ---p 0018f000 00:18 49184804 /software/fftw-3.2.2_intel_11.0.069/lib/libfftw3f.so.3.2.4 2b0e5b94b000-2b0e5b958000 rw-p 0018e000 00:18 49184804 /software/fftw-3.2.2_intel_11.0.069/lib/libfftw3f.so.3.2.4 2b0e5b958000-2b0e5b959000 rw-p 2b0e5b958000 00:00 0 2b0e5b96d000-2b0e5b96e000 rw-p 2b0e5b96d000 00:00 0 2b0e5b96e000-2b0e5000 r-xp 00:18 20054224 /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libgmx.so.6.0.0 2b0e5000-2b0e5bdbb000 ---p 0024d000 00:18 20054224 /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libgmx.so.6.0.0 2b0e5bdbb000-2b0e5bdcd000 rw-p 0024d000 00:18 20054224 /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libgmx.so.6.0.0 2b0e5bdcd000-2b0e5bdce000 rw-p 2b0e5bdcd000 00:00 0 2b0e5bdce000-2b0e5c0b7000 r-xp 00:17 6031605 /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_lp64.so 2b0e5c0b7000-2b0e5c1b6000 ---p 002e9000 00:17 6031605 /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_lp64.so 2b0e5c1b6000-2b0e5c1c1000 rw-p 002e8000 00:17 6031605 /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_lp64.so 2b0e5c1c1000-2b0e5c1c9000 rw-p 2b0e5c1c1000 00:00 0 2b0e5c1c9000-2b0e5c8c6000 r-xp 00:17 6031615 /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so 2b0e5c8c6000-2b0e5c9c6000 ---p 006fd000 00:17 6031615 /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so 2b0e5c9c6000-2b0e5c9d2000 rw-p 006fd000 00:17 6031615 /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so 2b0e5c9d2000-2b0e5c9dd000 rw-p 2b0e5c9d2000 00:00 0 2b0e5c9dd000-2b0e5cc7a000 r-xp 00:17 6031599 /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so 2b0e5cc7a000-2b0e5cd7a000 ---p 0029d000 00:17 6031599 /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so 2b0e5cd7a000-2b0e5cd7f000 rw-p 0029d000 00:17 6031599 /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so 2b0e5cd7f000-2b0e5cd92000 rw-p 2b0e5cd7f000 00:00 0 2b0e5cd92000-2b0e5cfe2000 r-xp 00:17 6783119 /opt/intel/Compiler/11.1/073/lib/intel64/libimf.so 2b0e5cfe2000-2b0e5d0e1000 ---p 0025 00:17 6783119 /opt/intel/Compiler/11.1/073/lib/intel64/libimf.so 2b0e5d0e1000-2b0e5d126000 rw-p 0024f000 00:17 6783119 /opt/intel/Compiler/11.1/073/lib/intel64/libimf.so 2b0e5d126000-2b0e5d23c000 r-xp 00:17 6783139 /opt/intel/Compiler/11.1/073/lib/intel64/libsvml.so 2b0e5d23c000-2b0e5d33b000 ---p 00116000 00:17 6783139 /opt/intel/Compiler/11.1/073/lib/intel64/libsvml.so 2b0e5d33b000-2b0e5d33c000 rw-p 00115000 00:17 6783139 /opt/intel/Compiler/11.1/073/lib/intel64/libsvml.so 2b0e5d33c000-2b0e5d377000 r-xp 00:17 6783121 /opt/intel/Compiler/11.1/073/lib/intel64/libintlc.so.5 2b0e5d377000-2b0e5d476000 ---p 0003b000 00:17 6783121 /opt/intel/Compiler/11.1/073/lib/intel64/libintlc.so.5 2b0e5d476000-2b0e5d479000 rw-p 0003a000 00:17 6783121 /opt/intel/Compiler/11.1/073/lib/intel64/libintlc.so.5 2b0e5d479000-2b0e5d8b9000 rw-p 2b0e5d479000 00:00 0 2b0e6000-2b0e60021000 rw-p 2b0e6000 00:00 0 2b0e60021000-2b0e6400 ---p 2b0e60021000 00:00 0 7fff4fa96000-7fff4faaa000 rwxp 7ffe9000 00:00 0 [stack] 7fff4faaa000-7fff4faac000 rw-p 7fffd000 00:00 0 ff60-ffe0 ---p 00:00 0 [vdso] Aborted On Wed, Feb 16, 2011 at 2:08 PM, Gerrit Groenhof ggro...@gwdg.de wrote: Are you trying to run with more than one thread? If so, try mdrun -nt 1 Gerrit 1. Re: gromacs QM/MM compilation with gaussian (Txema Mercero) 2. Re: Periodic Boundary Conditions g_mindist -pi (ifat shub) 3. Re: Re: Periodic Boundary Conditions g_mindist -pi (Mark Abraham) -- Message: 1 Date: Wed, 16 Feb 2011 12:23:49 +0100 From: Txema Mercero jm.merc...@ehu.es Subject: [gmx-users] Re: gromacs QM/MM compilation with gaussian To: gmx-users@gromacs.org Cc: Edu Ogando edu.oga...@ehu.es, Jon I?aki Mujika joni.muj...@ehu.es Message-ID: AANLkTi=o7w8cbez90u-vzk+q+46ehh+rrtrthgvuq...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi there! We are trying
