What is your path to the gaussian executable? 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 = 50000000 > 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) = 1.00000e+02 > Number of steps = 1000 > *** glibc detected *** > /software/gromacs-4.5.3-shared-ifort11_gauss/bin/mdrun: malloc(): > memory corruption: 0x00000000077711b0 *** > ======= 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: ======== > 00400000-0046d000 r-xp 00000000 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] > 3ddc800000-3ddc81c000 r-xp 00000000 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 > 3ddcc00000-3ddcd4c000 r-xp 00000000 08:02 5750905 > /lib64/libc-2.5.so > 3ddcd4c000-3ddcf4c000 ---p 0014c000 08:02 5750905 > /lib64/libc-2.5.so > 3ddcf4c000-3ddcf50000 r--p 0014c000 08:02 5750905 > /lib64/libc-2.5.so > 3ddcf50000-3ddcf51000 rw-p 00150000 08:02 5750905 > /lib64/libc-2.5.so > 3ddcf51000-3ddcf56000 rw-p 3ddcf51000 00:00 0 > 3ddd000000-3ddd082000 r-xp 00000000 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 > 3ddd400000-3ddd402000 r-xp 00000000 08:02 5750939 > /lib64/libdl-2.5.so > 3ddd402000-3ddd602000 ---p 00002000 08:02 5750939 > /lib64/libdl-2.5.so > 3ddd602000-3ddd603000 r--p 00002000 08:02 5750939 > /lib64/libdl-2.5.so > 3ddd603000-3ddd604000 rw-p 00003000 08:02 5750939 > /lib64/libdl-2.5.so > 3ddd800000-3ddd816000 r-xp 00000000 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 > 3dddc00000-3dddc14000 r-xp 00000000 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 > 3ddfc00000-3ddfc15000 r-xp 00000000 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 > 3de4400000-3de4533000 r-xp 00000000 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 > 3dea200000-3dea20d000 r-xp 00000000 08:02 5751072 > /lib64/libgcc_s-4.1.2-20080825.so.1 > 3dea20d000-3dea40d000 ---p 0000d000 08:02 5751072 > /lib64/libgcc_s-4.1.2-20080825.so.1 > 3dea40d000-3dea40e000 rw-p 0000d000 08:02 5751072 > /lib64/libgcc_s-4.1.2-20080825.so.1 > 2b0e5affe000-2b0e5b000000 rw-p 2b0e5affe000 00:00 0 > 2b0e5b000000-2b0e5b07e000 r-xp 00000000 00:18 20054237 > /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libgmxpreprocess.so.6.0.0 > 2b0e5b07e000-2b0e5b27d000 ---p 0007e000 00:18 20054237 > /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libgmxpreprocess.so.6.0.0 > 2b0e5b27d000-2b0e5b280000 rw-p 0007d000 00:18 20054237 > /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libgmxpreprocess.so.6.0.0 > 2b0e5b280000-2b0e5b2ae000 rw-p 2b0e5b280000 00:00 0 > 2b0e5b2ae000-2b0e5b3b9000 r-xp 00000000 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 00000000 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 > 2b0e5b96e000-2b0e5bbbb000 r-xp 00000000 00:18 20054224 > /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libgmx.so.6.0.0 > 2b0e5bbbb000-2b0e5bdbb000 ---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 00000000 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 00000000 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 00000000 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 00000000 00:17 6783119 > /opt/intel/Compiler/11.1/073/lib/intel64/libimf.so > 2b0e5cfe2000-2b0e5d0e1000 ---p 00250000 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 00000000 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 00000000 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 > 2b0e60000000-2b0e60021000 rw-p 2b0e60000000 00:00 0 > 2b0e60021000-2b0e64000000 ---p 2b0e60021000 00:00 0 > 7fff4fa96000-7fff4faaa000 rwxp 7ffffffe9000 00:00 0 > [stack] > 7fff4faaa000-7fff4faac000 rw-p 7fffffffd000 00:00 0 > ffffffffff600000-ffffffffffe00000 ---p 00000000 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 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 >>> >>> >>> ------------------------------ >>> >>> Message: 2 >>> Date: Wed, 16 Feb 2011 13:30:29 +0200 >>> From: ifat shub <shubi...@gmail.com> >>> Subject: [gmx-users] Re: Periodic Boundary Conditions g_mindist -pi >>> To: gmx-users@gromacs.org >>> Message-ID: >>> <AANLkTi=71Moj0kH4=tr3_gdh54b1wsnei0hundx++...@mail.gmail.com> >>> Content-Type: text/plain; charset="iso-8859-1" >>> >>> Hi Tsjerk, >>> Thank you for your reply. >>> I am aware of the trajconv option but I wanted to know if there is a way to >>> avoid these kind of jumps over the periodic boundaries during the mdrun and >>> not post process? >>> Thanks, >>> Ifat >>> >>> message: 4 >>>> Date: Wed, 16 Feb 2011 11:19:14 +0200 >>>> From: ifat shub <shubi...@gmail.com> >>>> Subject: [gmx-users] Periodic Boundary Conditions g_mindist -pi >>>> To: gmx-users@gromacs.org >>>> Message-ID: >>>> <AANLkTi=sgjftmrf-0nvmzzogfs+xhyxv5u6ggfnhr...@mail.gmail.com> >>>> Content-Type: text/plain; charset="iso-8859-1" >>>> >>>> Hi, >>>> >>>> >>>> >>>> I am running a simulation on the complex 1aik.pdb in 310K. I wanted to see >>>> if the complex is seeing its next periodic image, so I used the g_mindist >>>> command with the -pi option. My command line was: >>>> >>>> g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi >>>> >>>> The output (see below) was stable until ~344ps when there is a jump in the >>>> max internal distance (third column) from ~6nm to ~22nm. After the jump the >>>> numbers are reduced back to ~6nm and remained stable until the run is >>>> completed at 1ns. >>>> >>>> Does anyone know how to explain this jump? Is this a real problem or just a >>>> visualization artifact? Is there a way to avoid such jumps? >>>> >>>> >>>> >>>> Here is the mdp file I used: >>>> >>>> ------run.mdp------ >>>> >>>> integrator = md >>>> >>>> nsteps = 1000000 >>>> >>>> dt = 0.001 >>>> >>>> coulombtype = pme >>>> >>>> vdw-type = cut-off >>>> >>>> tcoupl = Berendsen >>>> >>>> tc-grps = protein non-protein >>>> >>>> tau-t = 0.1 0.1 >>>> >>>> ref-t = 310 310 >>>> >>>> nstxout = 100 >>>> >>>> nstvout = 0 >>>> >>>> nstxtcout = 100 >>>> >>>> nstenergy = 100 >>>> >>>> comm_mode = Linear ; Angular >>>> >>>> comm_grps = Protein >>>> >>>> xtc_grps = Protein >>>> >>>> energygrps = Protein >>>> >>>> ------------------ >>>> >>>> >>>> >>>> Thanks, >>>> >>>> Ifat >>>> >>>> >>>> >>>> The output: >>>> >>>> 343.7 10.813 5.924 16.445 16.445 16.445 >>>> >>>> 343.8 10.809 5.949 16.445 16.445 16.445 >>>> >>>> 343.9 10.804 5.959 16.445 16.445 16.445 >>>> >>>> 344 10.808 5.974 16.445 16.445 16.445 >>>> >>>> 344.1 0.18 21.982 16.445 16.445 16.445 >>>> >>>> 344.2 10.778 5.977 16.445 16.445 16.445 >>>> >>>> 344.3 10.768 5.996 16.445 16.445 16.445 >>>> >>>> 344.4 10.764 6.016 16.445 16.445 16.445 >>>> >>>> 344.5 10.722 6.029 16.445 16.445 16.445 >>>> >>>> 344.6 10.774 6.01 16.445 16.445 16.445 >>>> >>>> 344.7 0.174 21.984 16.445 16.445 16.445 >>>> >>>> 344.8 0.176 21.98 16.445 16.445 16.445 >>>> >>>> 344.9 0.17 22.002 16.445 16.445 16.445 >>>> >>>> 345 0.173 21.981 16.445 16.445 16.445 >>>> >>>> 345.1 0.191 21.954 16.445 16.445 16.445 >>>> >>>> 345.2 0.183 21.958 16.445 16.445 16.445 >>>> >>>> 345.3 0.181 22.012 16.445 16.445 16.445 >>>> >>>> 345.4 0.17 22.054 16.445 16.445 16.445 >>>> >>>> 345.5 0.168 22.054 16.445 16.445 16.445 >>>> >>>> 345.6 0.189 22.039 16.445 16.445 16.445 >>>> >>>> 345.7 0.171 22.007 16.445 16.445 16.445 >>>> >>>> 345.8 0.186 22.031 16.445 16.445 16.445 >>>> >>>> 345.9 0.171 22.077 16.445 16.445 16.445 >>>> >>>> 346 0.187 21.99 16.445 16.445 16.445 >>>> >>>> 346.1 0.173 21.984 16.445 16.445 16.445 >>>> >>>> 346.2 0.181 22.02 16.445 16.445 16.445 >>>> >>>> 346.3 10.82 5.984 16.445 16.445 16.445 >>>> >>>> 346.4 10.81 6.002 16.445 16.445 16.445 >>>> >>>> 346.5 10.819 6.008 16.445 16.445 16.445 >>>> >>>> 346.6 10.813 5.996 16.445 16.445 16.445 >>>> >>>> 346.7 10.781 6.006 16.445 16.445 16.445 >>>> >>>> 346.8 10.793 6.026 16.445 16.445 16.445 >>>> >>>> 346.9 10.745 5.985 16.445 16.445 16.445 >>>> >>>> 347 10.762 5.999 16.445 16.445 16.445 >>>> >>>> 347.1 10.781 5.984 16.445 16.445 16.445 >>>> >>>> 347.2 10.784 6.002 16.445 16.445 16.445 >>>> -------------- next part -------------- >>>> An HTML attachment was scrubbed... >>>> URL: >>>> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/8495d798/attachment-0001.html >>>> >>>> ------------------------------ >>>> >>>> Message: 5 >>>> Date: Wed, 16 Feb 2011 10:43:56 +0100 >>>> From: Tsjerk Wassenaar <tsje...@gmail.com> >>>> Subject: Re: [gmx-users] Periodic Boundary Conditions g_mindist -pi >>>> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >>>> Message-ID: >>>> <AANLkTinr05YyKV7rqzCSwEch=abxfur+adkenmxem...@mail.gmail.com> >>>> Content-Type: text/plain; charset=ISO-8859-1 >>>> >>>> Hi Ifat, >>>> >>>> I guess this is a jump over the periodic boundaries. You should remove >>>> jumps from the trajectory (-pbc nojump) before running g_mindist -pi. >>>> >>>> Cheers, >>>> >>>> Tsjerk >>>> >>>> On Wed, Feb 16, 2011 at 10:19 AM, ifat shub <shubi...@gmail.com> wrote: >>>>> Hi, >>>>> >>>>> >>>>> >>>>> I am running a simulation on the complex 1aik.pdb in 310K. I wanted to >>>> see >>>>> if the complex is seeing its next periodic image, so I used the g_mindist >>>>> command with the -pi option. My command line was: >>>>> >>>>> g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi >>>>> >>>>> The output (see below) was stable until ~344ps when there is a jump in >>>> the >>>>> max internal distance (third column) from ~6nm to ~22nm. After the jump >>>> the >>>>> numbers are reduced back to ~6nm and remained stable until the run is >>>>> completed at 1ns. >>>>> >>>>> Does anyone know how to explain this jump? Is this a real problem or just >>>> a >>>>> visualization artifact? Is there a way to avoid such jumps? >>>>> >>>>> >>>>> >>>>> Here is the mdp file I used: >>>>> >>>>> ------run.mdp------ >>>>> >>>>> integrator = md >>>>> >>>>> nsteps = 1000000 >>>>> >>>>> dt = 0.001 >>>>> >>>>> coulombtype = pme >>>>> >>>>> vdw-type = cut-off >>>>> >>>>> tcoupl = Berendsen >>>>> >>>>> tc-grps = protein non-protein >>>>> >>>>> tau-t = 0.1 0.1 >>>>> >>>>> ref-t = 310 310 >>>>> >>>>> nstxout = 100 >>>>> >>>>> nstvout = 0 >>>>> >>>>> nstxtcout = 100 >>>>> >>>>> nstenergy = 100 >>>>> >>>>> comm_mode = Linear ; Angular >>>>> >>>>> comm_grps = Protein >>>>> >>>>> xtc_grps = Protein >>>>> >>>>> energygrps = Protein >>>>> >>>>> ------------------ >>>>> >>>>> >>>>> >>>>> Thanks, >>>>> >>>>> Ifat >>>>> >>>>> >>>>> >>>>> The output: >>>>> >>>>> 343.7 10.813 5.924 16.445 16.445 16.445 >>>>> >>>>> 343.8 10.809 5.949 16.445 16.445 16.445 >>>>> >>>>> 343.9 10.804 5.959 16.445 16.445 16.445 >>>>> >>>>> 344 10.808 5.974 16.445 16.445 16.445 >>>>> >>>>> 344.1 0.18 21.982 16.445 16.445 16.445 >>>>> >>>>> 344.2 10.778 5.977 16.445 16.445 16.445 >>>>> >>>>> 344.3 10.768 5.996 16.445 16.445 16.445 >>>>> >>>>> 344.4 10.764 6.016 16.445 16.445 16.445 >>>>> >>>>> 344.5 10.722 6.029 16.445 16.445 16.445 >>>>> >>>>> 344.6 10.774 6.01 16.445 16.445 16.445 >>>>> >>>>> 344.7 0.174 21.984 16.445 16.445 16.445 >>>>> >>>>> 344.8 0.176 21.98 16.445 16.445 16.445 >>>>> >>>>> 344.9 0.17 22.002 16.445 16.445 16.445 >>>>> >>>>> 345 0.173 21.981 16.445 16.445 16.445 >>>>> >>>>> 345.1 0.191 21.954 16.445 16.445 16.445 >>>>> >>>>> 345.2 0.183 21.958 16.445 16.445 16.445 >>>>> >>>>> 345.3 0.181 22.012 16.445 16.445 16.445 >>>>> >>>>> 345.4 0.17 22.054 16.445 16.445 16.445 >>>>> >>>>> 345.5 0.168 22.054 16.445 16.445 16.445 >>>>> >>>>> 345.6 0.189 22.039 16.445 16.445 16.445 >>>>> >>>>> 345.7 0.171 22.007 16.445 16.445 16.445 >>>>> >>>>> 345.8 0.186 22.031 16.445 16.445 16.445 >>>>> >>>>> 345.9 0.171 22.077 16.445 16.445 16.445 >>>>> >>>>> 346 0.187 21.99 16.445 16.445 16.445 >>>>> >>>>> 346.1 0.173 21.984 16.445 16.445 16.445 >>>>> >>>>> 346.2 0.181 22.02 16.445 16.445 16.445 >>>>> >>>>> 346.3 10.82 5.984 16.445 16.445 16.445 >>>>> >>>>> 346.4 10.81 6.002 16.445 16.445 16.445 >>>>> >>>>> 346.5 10.819 6.008 16.445 16.445 16.445 >>>>> >>>>> 346.6 10.813 5.996 16.445 16.445 16.445 >>>>> >>>>> 346.7 10.781 6.006 16.445 16.445 16.445 >>>>> >>>>> 346.8 10.793 6.026 16.445 16.445 16.445 >>>>> >>>>> 346.9 10.745 5.985 16.445 16.445 16.445 >>>>> >>>>> 347 10.762 5.999 16.445 16.445 16.445 >>>>> >>>>> 347.1 10.781 5.984 16.445 16.445 16.445 >>>>> >>>>> 347.2 10.784 6.002 16.445 16.445 16.445 >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> 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 >>>>> >>>> >>>> >>>> >>>> -- >>>> Tsjerk A. Wassenaar, Ph.D. >>>> >>>> post-doctoral researcher >>>> Molecular Dynamics Group >>>> * Groningen Institute for Biomolecular Research and Biotechnology >>>> * Zernike Institute for Advanced Materials >>>> University of Groningen >>>> The Netherlands >>>> >>>> >>>> ------------------------------ >>>> >>>> -- >>>> 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 82, Issue 125 >>>> ****************************************** >>>> >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: >>> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/daa11467/attachment-0001.html >>> >>> ------------------------------ >>> >>> Message: 3 >>> Date: Wed, 16 Feb 2011 23:00:32 +1100 >>> From: Mark Abraham <mark.abra...@anu.edu.au> >>> Subject: Re: [gmx-users] Re: Periodic Boundary Conditions g_mindist >>> -pi >>> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >>> Message-ID: <4d5bbc60.5080...@anu.edu.au> >>> Content-Type: text/plain; charset="iso-8859-1" >>> >>> On 16/02/2011 10:30 PM, ifat shub wrote: >>>> >>>> Hi Tsjerk, >>>> Thank you for your reply. >>>> I am aware of the trajconv option but I wanted to know if there is a >>>> way to avoid these kind of jumps over the periodic boundaries during >>>> the mdrun and not post process? >>> >>> No. mdrun does not know in advance what your visualization requirements >>> are, and frankly there are better things to do with expensive compute >>> cluster time. Post-processing a small number of frames elsewhere is much >>> better use of resources. >>> >>> Mark >>> >>> >>>> message: 4 >>>> Date: Wed, 16 Feb 2011 11:19:14 +0200 >>>> From: ifat shub <shubi...@gmail.com <mailto:shubi...@gmail.com>> >>>> Subject: [gmx-users] Periodic Boundary Conditions g_mindist -pi >>>> To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org> >>>> Message-ID: >>>> <AANLkTi=sgjftmrf-0nvmzzogfs+xhyxv5u6ggfnhr...@mail.gmail.com >>>> <mailto:sgjftmrf-0nvmzzogfs%2bxhyxv5u6ggfnhr...@mail.gmail.com>> >>>> Content-Type: text/plain; charset="iso-8859-1" >>>> >>>> Hi, >>>> >>>> >>>> >>>> I am running a simulation on the complex 1aik.pdb in 310K. I >>>> wanted to see >>>> if the complex is seeing its next periodic image, so I used the >>>> g_mindist >>>> command with the -pi option. My command line was: >>>> >>>> g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi >>>> >>>> The output (see below) was stable until ~344ps when there is a >>>> jump in the >>>> max internal distance (third column) from ~6nm to ~22nm. After the >>>> jump the >>>> numbers are reduced back to ~6nm and remained stable until the run is >>>> completed at 1ns. >>>> >>>> Does anyone know how to explain this jump? Is this a real problem >>>> or just a >>>> visualization artifact? Is there a way to avoid such jumps? >>>> >>>> >>>> >>>> Here is the mdp file I used: >>>> >>>> ------run.mdp------ >>>> >>>> integrator = md >>>> >>>> nsteps = 1000000 >>>> >>>> dt = 0.001 >>>> >>>> coulombtype = pme >>>> >>>> vdw-type = cut-off >>>> >>>> tcoupl = Berendsen >>>> >>>> tc-grps = protein non-protein >>>> >>>> tau-t = 0.1 0.1 >>>> >>>> ref-t = 310 310 >>>> >>>> nstxout = 100 >>>> >>>> nstvout = 0 >>>> >>>> nstxtcout = 100 >>>> >>>> nstenergy = 100 >>>> >>>> comm_mode = Linear ; Angular >>>> >>>> comm_grps = Protein >>>> >>>> xtc_grps = Protein >>>> >>>> energygrps = Protein >>>> >>>> ------------------ >>>> >>>> >>>> >>>> Thanks, >>>> >>>> Ifat >>>> >>>> >>>> >>>> The output: >>>> >>>> 343.7 10.813 5.924 16.445 16.445 16.445 >>>> >>>> 343.8 10.809 5.949 16.445 16.445 16.445 >>>> >>>> 343.9 10.804 5.959 16.445 16.445 16.445 >>>> >>>> 344 10.808 5.974 16.445 16.445 16.445 >>>> >>>> 344.1 0.18 21.982 16.445 16.445 16.445 >>>> >>>> 344.2 10.778 5.977 16.445 16.445 16.445 >>>> >>>> 344.3 10.768 5.996 16.445 16.445 16.445 >>>> >>>> 344.4 10.764 6.016 16.445 16.445 16.445 >>>> >>>> 344.5 10.722 6.029 16.445 16.445 16.445 >>>> >>>> 344.6 10.774 6.01 16.445 16.445 16.445 >>>> >>>> 344.7 0.174 21.984 16.445 16.445 16.445 >>>> >>>> 344.8 0.176 21.98 16.445 16.445 16.445 >>>> >>>> 344.9 0.17 22.002 16.445 16.445 16.445 >>>> >>>> 345 0.173 21.981 16.445 16.445 16.445 >>>> >>>> 345.1 0.191 21.954 16.445 16.445 16.445 >>>> >>>> 345.2 0.183 21.958 16.445 16.445 16.445 >>>> >>>> 345.3 0.181 22.012 16.445 16.445 16.445 >>>> >>>> 345.4 0.17 22.054 16.445 16.445 16.445 >>>> >>>> 345.5 0.168 22.054 16.445 16.445 16.445 >>>> >>>> 345.6 0.189 22.039 16.445 16.445 16.445 >>>> >>>> 345.7 0.171 22.007 16.445 16.445 16.445 >>>> >>>> 345.8 0.186 22.031 16.445 16.445 16.445 >>>> >>>> 345.9 0.171 22.077 16.445 16.445 16.445 >>>> >>>> 346 0.187 21.99 16.445 16.445 16.445 >>>> >>>> 346.1 0.173 21.984 16.445 16.445 16.445 >>>> >>>> 346.2 0.181 22.02 16.445 16.445 16.445 >>>> >>>> 346.3 10.82 5.984 16.445 16.445 16.445 >>>> >>>> 346.4 10.81 6.002 16.445 16.445 16.445 >>>> >>>> 346.5 10.819 6.008 16.445 16.445 16.445 >>>> >>>> 346.6 10.813 5.996 16.445 16.445 16.445 >>>> >>>> 346.7 10.781 6.006 16.445 16.445 16.445 >>>> >>>> 346.8 10.793 6.026 16.445 16.445 16.445 >>>> >>>> 346.9 10.745 5.985 16.445 16.445 16.445 >>>> >>>> 347 10.762 5.999 16.445 16.445 16.445 >>>> >>>> 347.1 10.781 5.984 16.445 16.445 16.445 >>>> >>>> 347.2 10.784 6.002 16.445 16.445 16.445 >>>> -------------- next part -------------- >>>> An HTML attachment was scrubbed... >>>> URL: >>>> >>>> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/8495d798/attachment-0001.html >>>> >>>> ------------------------------ >>>> >>>> Message: 5 >>>> Date: Wed, 16 Feb 2011 10:43:56 +0100 >>>> From: Tsjerk Wassenaar <tsje...@gmail.com <mailto:tsje...@gmail.com>> >>>> Subject: Re: [gmx-users] Periodic Boundary Conditions g_mindist -pi >>>> To: Discussion list for GROMACS users <gmx-users@gromacs.org >>>> <mailto:gmx-users@gromacs.org>> >>>> Message-ID: >>>> <AANLkTinr05YyKV7rqzCSwEch=abxfur+adkenmxem...@mail.gmail.com >>>> <mailto:abxfur%2badkenmxem...@mail.gmail.com>> >>>> Content-Type: text/plain; charset=ISO-8859-1 >>>> >>>> Hi Ifat, >>>> >>>> I guess this is a jump over the periodic boundaries. You should remove >>>> jumps from the trajectory (-pbc nojump) before running g_mindist -pi. >>>> >>>> Cheers, >>>> >>>> Tsjerk >>>> >>>> On Wed, Feb 16, 2011 at 10:19 AM, ifat shub <shubi...@gmail.com >>>> <mailto:shubi...@gmail.com>> wrote: >>>>> Hi, >>>>> >>>>> >>>>> >>>>> I am running a simulation on the complex 1aik.pdb in 310K. I >>>> wanted to see >>>>> if the complex is seeing its next periodic image, so I used the >>>> g_mindist >>>>> command with the -pi option. My command line was: >>>>> >>>>> g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi >>>>> >>>>> The output (see below) was stable until ~344ps when there is a >>>> jump in the >>>>> max internal distance (third column) from ~6nm to ~22nm. After >>>> the jump the >>>>> numbers are reduced back to ~6nm and remained stable until the >>>> run is >>>>> completed at 1ns. >>>>> >>>>> Does anyone know how to explain this jump? Is this a real >>>> problem or just a >>>>> visualization artifact? Is there a way to avoid such jumps? >>>>> >>>>> >>>>> >>>>> Here is the mdp file I used: >>>>> >>>>> ------run.mdp------ >>>>> >>>>> integrator = md >>>>> >>>>> nsteps = 1000000 >>>>> >>>>> dt = 0.001 >>>>> >>>>> coulombtype = pme >>>>> >>>>> vdw-type = cut-off >>>>> >>>>> tcoupl = Berendsen >>>>> >>>>> tc-grps = protein non-protein >>>>> >>>>> tau-t = 0.1 0.1 >>>>> >>>>> ref-t = 310 310 >>>>> >>>>> nstxout = 100 >>>>> >>>>> nstvout = 0 >>>>> >>>>> nstxtcout = 100 >>>>> >>>>> nstenergy = 100 >>>>> >>>>> comm_mode = Linear ; Angular >>>>> >>>>> comm_grps = Protein >>>>> >>>>> xtc_grps = Protein >>>>> >>>>> energygrps = Protein >>>>> >>>>> ------------------ >>>>> >>>>> >>>>> >>>>> Thanks, >>>>> >>>>> Ifat >>>>> >>>>> >>>>> >>>>> The output: >>>>> >>>>> 343.7 10.813 5.924 16.445 16.445 16.445 >>>>> >>>>> 343.8 10.809 5.949 16.445 16.445 16.445 >>>>> >>>>> 343.9 10.804 5.959 16.445 16.445 16.445 >>>>> >>>>> 344 10.808 5.974 16.445 16.445 16.445 >>>>> >>>>> 344.1 0.18 21.982 16.445 16.445 16.445 >>>>> >>>>> 344.2 10.778 5.977 16.445 16.445 16.445 >>>>> >>>>> 344.3 10.768 5.996 16.445 16.445 16.445 >>>>> >>>>> 344.4 10.764 6.016 16.445 16.445 16.445 >>>>> >>>>> 344.5 10.722 6.029 16.445 16.445 16.445 >>>>> >>>>> 344.6 10.774 6.01 16.445 16.445 16.445 >>>>> >>>>> 344.7 0.174 21.984 16.445 16.445 16.445 >>>>> >>>>> 344.8 0.176 21.98 16.445 16.445 16.445 >>>>> >>>>> 344.9 0.17 22.002 16.445 16.445 16.445 >>>>> >>>>> 345 0.173 21.981 16.445 16.445 16.445 >>>>> >>>>> 345.1 0.191 21.954 16.445 16.445 16.445 >>>>> >>>>> 345.2 0.183 21.958 16.445 16.445 16.445 >>>>> >>>>> 345.3 0.181 22.012 16.445 16.445 16.445 >>>>> >>>>> 345.4 0.17 22.054 16.445 16.445 16.445 >>>>> >>>>> 345.5 0.168 22.054 16.445 16.445 16.445 >>>>> >>>>> 345.6 0.189 22.039 16.445 16.445 16.445 >>>>> >>>>> 345.7 0.171 22.007 16.445 16.445 16.445 >>>>> >>>>> 345.8 0.186 22.031 16.445 16.445 16.445 >>>>> >>>>> 345.9 0.171 22.077 16.445 16.445 16.445 >>>>> >>>>> 346 0.187 21.99 16.445 16.445 16.445 >>>>> >>>>> 346.1 0.173 21.984 16.445 16.445 16.445 >>>>> >>>>> 346.2 0.181 22.02 16.445 16.445 16.445 >>>>> >>>>> 346.3 10.82 5.984 16.445 16.445 16.445 >>>>> >>>>> 346.4 10.81 6.002 16.445 16.445 16.445 >>>>> >>>>> 346.5 10.819 6.008 16.445 16.445 16.445 >>>>> >>>>> 346.6 10.813 5.996 16.445 16.445 16.445 >>>>> >>>>> 346.7 10.781 6.006 16.445 16.445 16.445 >>>>> >>>>> 346.8 10.793 6.026 16.445 16.445 16.445 >>>>> >>>>> 346.9 10.745 5.985 16.445 16.445 16.445 >>>>> >>>>> 347 10.762 5.999 16.445 16.445 16.445 >>>>> >>>>> 347.1 10.781 5.984 16.445 16.445 16.445 >>>>> >>>>> 347.2 10.784 6.002 16.445 16.445 16.445 >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> gmx-users mailing list gmx-users@gromacs.org >>>> <mailto: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 >>>> <mailto:gmx-users-requ...@gromacs.org>. >>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>> >>>> >>>> >>>> >>>> -- >>>> Tsjerk A. Wassenaar, Ph.D. >>>> >>>> post-doctoral researcher >>>> Molecular Dynamics Group >>>> * Groningen Institute for Biomolecular Research and Biotechnology >>>> * Zernike Institute for Advanced Materials >>>> University of Groningen >>>> The Netherlands >>>> >>>> >>>> ------------------------------ >>>> >>>> -- >>>> gmx-users mailing list >>>> gmx-users@gromacs.org <mailto: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 82, Issue 125 >>>> ****************************************** >>>> >>>> >>> >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: >>> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/1ab1794a/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 82, Issue 127 >>> ****************************************** >> >> -- >> 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
