Dear Justin, Thanks for the response.
Here is the info regarding the cluster where gromacs version 4.0.5 is installed with icc compliers. $ ./configure --prefix=/usr/local/gromacs --enable-mpi --with-fft=fftw2 uname -m = x86_64 uname -r = 2.6.18-128.7.1.el5 uname -s = Linux uname -v = #1 SMP Mon Aug 24 08:21:56 EDT 2009 compilers: C and fortran Intel 10.1 Please suggest me as the grompp command also donot work with this configuration. Thanks, Ram On Mon, Jan 4, 2010 at 6:17 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > ram bio wrote: >> >> Dear Justin, >> >> Thanks for the response. >> >> I am using gromacs 4.0.3 version on my PC and 4.0.5 on cluster, I have >> asked my system admin to provide the details regarding the cluster, >> whereas for my PC: >> >> The info is as follows: >> >> 1. The Gromacs version you are using. - 4.0.3 >> 2. The compilers used in installing Gromacs.- gcc >> gcc -v >> Using built-in specs. >> Target: i386-redhat-linux >> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man >> --infodir=/usr/share/info --enable-shared --enable-threads=posix >> --enable-checking=release --with-system-zlib --enable-__cxa_atexit >> --disable-libunwind-exceptions --enable-libgcj-multifile >> --enable-languages=c,c++,objc,obj-c++,java,fortran,ada >> --enable-java-awt=gtk --disable-dssi --enable-plugin >> --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre >> --with-cpu=generic --host=i386-redhat-linux >> Thread model: posix >> gcc version 4.1.2 20080704 (Red Hat 4.1.2-44) >> > > The gcc 4.1.x is well-known to be buggy, and as advised on the Gromacs > source code download site: > > "WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These > compilers come with recent Linux distrubutions like Fedora 5/6 etc." > > I would suggest updating to the latest version of Gromacs (4.0.7), using a > more reliable compiler (other versions of gcc, i.e. 4.0.x and older, and > 4.2.x and newer, are fine). > >> 3. Options specified during configuration. >> >> I didnot get this, can you please elaborate... >> > > Things like --enable-shared, --disable-(whatever), but I don't know that any > of this is relevant. I think the compiler is the problem. > > -Justin > >> >> 4. Specifications of your hardware. >> >> processor : 0 >> vendor_id : GenuineIntel >> cpu family : 6 >> model : 13 >> model name : Intel(R) Pentium(R) M processor 1.70GHz >> stepping : 6 >> cpu MHz : 600.000 >> cache size : 2048 KB >> fdiv_bug : no >> hlt_bug : no >> f00f_bug : no >> coma_bug : no >> fpu : yes >> fpu_exception : yes >> cpuid level : 2 >> wp : yes >> flags : fpu vme de pse tsc msr mce cx8 mtrr pge mca cmov pat >> clflush dts acpi mmx fxsr sse sse2 ss tm pbe up est tm2 >> bogomips : 1196.53 >> >> Linux version 2.6.18-8.el5 (mockbu...@builder4.centos.org) (gcc >> version 4.1.1 20070105 (Red Hat 4.1.1-52)) #1 SMP Thu Mar 15 19:57:35 >> EDT 2007 >> >> Build Operating System: Linux 2.6.18-53.1.14.el5PAE i686 Red Hat, Inc. >> Current Operating System: Linux localhost.localdomain 2.6.18-8.el5 #1 >> SMP Thu Mar 15 19:57:35 EDT 2007 i686 >> Build Date: 21 June 2008 >> Build ID: xorg-x11-server 1.1.1-48.41.el5_2.1 >> >> >> I would be providing the info about the cluster, once I receive it, >> mean please let me know if any info is missing and help me. >> >> Thanks, >> >> Ram >> >> >> >> >> >> On Thu, Dec 31, 2009 at 11:49 PM, Justin A. Lemkul <jalem...@vt.edu> >> wrote: >>> >>> ram bio wrote: >>>> >>>> Dear Gromacs Users, >>>> >>>> Iam following Drug/Enzyme complex solvation tutorial by John E. >>>> Kerrigan, I am unable to execute the grompp step as per the tutorial, >>>> the output of grompp command is as follows: >>>> >>>> grompp -f minim.mdp -c trp_b4ion.gro -p trp.top -o trp_b4ion.tpr >>>> >>>> >>>> :-) grompp (-: >>>> >>>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.11# >>>> checking input for internal consistency... >>>> processing topology... >>>> Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.itp >>>> Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6nb.itp >>>> Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6bon.itp >>>> Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp >>>> Segmentation fault >>>> >>>> what i have done is as per the tutorial, that is >>>> 1) generated the drg.itp using prodrug beta >>>> 2) executed pdb2gmx using 4 that is ff53a6 ff >>>> 3) edit the drg.itp by removing the lines redundant as per trp.top >>>> 4) edit trp.gro by adding drg coordinates and chainging the numbers >>>> >>>> please help me to overcome this error, for your convenience I have >>>> attached the drg.itp, trp.top, trp.gro and trp_b4ion.gro files. >>>> >>> I doubt any of these files will be useful. Better information would >>> include: >>> >>> 1. The Gromacs version you are using. >>> 2. The compilers used in installing Gromacs. >>> 3. Options specified during configuration. >>> 4. Specifications of your hardware. >>> >>> A segmentation fault is a memory error and can have numerous causes. The >>> above information may be useful. >>> >>> -Justin >>> >>>> Thanks, >>>> >>>> Ram >>>> 4 attachments — >>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> -- >>> 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/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/mailing_lists/users.php >>> >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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/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/mailing_lists/users.php > -- 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/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? 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