Re: [gmx-users] grimaces 4.6 installation error
On Fri, Feb 1, 2013 at 2:18 AM, Fernando Favela ffav...@fis.cinvestav.mxwrote: Dear Gromacs users, I'm trying to install GMX 4.6 in a 64 Bit Machine with Nvidia GTX 680 cards, I've already installed the intel compilers, cuda 5 and openmpi. I do the following procedure: CC=/opt/intel/bin/icc CXX=/opt/intel/bin/icpc cmake .. then sudo make -j 12 Don't use sudo before make. Consider using sudo before make install, per the installation instructions. There's no error message in the output file you posted. I suspect you might running sudo make, and then make and running into file permissions problems because of it. Remove your whole build directory (which will probably need sudo) and start again. Mark and I get this error: Linking CXX shared library libmd.so cd /home/ffavela/Downloads/gromacs-4.6/build-cmake/src/mdlib /usr/bin/cmake -E cmake_link_script CMakeFiles/md.dir/link.txt --verbose=1 /opt/intel/bin/icpc -fPIC -mavx -Wall -ip -funroll-all-loops -O3 -DNDEBUG -shared -Wl,-soname,libmd.so.6 -o libmd.so.6 CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_gpu_ref.c.o CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_simd_4xn.c.o CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_common.c.o CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_simd_2xnn.c.o CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_ref.c.o CMakeFiles/md.dir/genborn_allvsall.c.o CMakeFiles/md.dir/qm_mopac.c.o CMakeFiles/md.dir/mvxvf.c.o CMakeFiles/md.dir/genborn.c.o CMakeFiles/md.dir/ebin.c.o CMakeFiles/md.dir/csettle.c.o CMakeFiles/md.dir/genborn_allvsall_sse2_single.c.o CMakeFiles/md.dir/pme.c.o CMakeFiles/md.dir/gmx_fft.c.o CMakeFiles/md.dir/force.c.o CMakeFiles/md.dir/qm_gaussian.c.o CMakeFiles/md.dir/qm_orca.c.o CMakeFiles/md.dir/mdatom.c.o CMakeFiles/md.dir/stat.c.o CMakeFiles/md.dir/perf_est.c.o CMakeFiles/md.dir/domdec_network.c.o CMakeFiles/md.dir/pme_pp.c.o CMakeFiles/md.dir/calcmu.c.o CMakeFiles/md.dir/shakef.c.o CMakeFiles/md.dir/fft5d.c.o CMakeFiles/md.dir/tables.c.o CMakeFiles/md.dir/qmmm.c.o CMakeFiles/md.dir/domdec_con.c.o CMakeFiles/md.dir/clincs.c.o CMakeFiles/md.dir/domdec_setup.c.o CMakeFiles/md.dir/gmx_wallcycle.c.o CMakeFiles/md.dir/gmx_fft_fftw3.c.o CMakeFiles/md.dir/partdec.c.o CMakeFiles/md.dir/domdec.c.o CMakeFiles/md.dir/genborn_allvsall_sse2_double.c.o CMakeFiles/md.dir/md_support.c.o CMakeFiles/md.dir/vsite.c.o CMakeFiles/md.dir/groupcoord.c.o CMakeFiles/md.dir/mdebin.c.o CMakeFiles/md.dir/gmx_fft_fftpack.c.o CMakeFiles/md.dir/tgroup.c.o CMakeFiles/md.dir/vcm.c.o CMakeFiles/md.dir/nsgrid.c.o CMakeFiles/md.dir/nbnxn_search.c.o CMakeFiles/md.dir/constr.c.o CMakeFiles/md.dir/shellfc.c.o CMakeFiles/md.dir/iteratedconstraints.c.o CMakeFiles/md.dir/rf_util.c.o CMakeFiles/md.dir/update.c.o CMakeFiles/md.dir/genborn_sse2_double.c.o CMakeFiles/md.dir/forcerec.c.o CMakeFiles/md.dir/nbnxn_atomdata.c.o CMakeFiles/md.dir/genborn_sse2_single.c.o CMakeFiles/md.dir/gmx_fft_mkl.c.o CMakeFiles/md.dir/pull.c.o CMakeFiles/md.dir/domdec_box.c.o CMakeFiles/md.dir/domdec_top.c.o CMakeFiles/md.dir/mdebin_bar.c.o CMakeFiles/md.dir/nlistheuristics.c.o CMakeFiles/md.dir/qm_gamess.c.o CMakeFiles/md.dir/coupling.c.o CMakeFiles/md.dir/adress.c.o CMakeFiles/md.dir/init.c.o CMakeFiles/md.dir/wnblist.c.o CMakeFiles/md.dir/expanded.c.o CMakeFiles/md.dir/wall.c.o CMakeFiles/md.dir/ns.c.o CMakeFiles/md.dir/minimize.c.o CMakeFiles/md.dir/sim_util.c.o CMakeFiles/md.dir/pullutil.c.o CMakeFiles/md.dir/gmx_parallel_3dfft.c.o CMakeFiles/md.dir/edsam.c.o CMakeFiles/md.dir/pull_rotation.c.o CMakeFiles/md.dir/gmx_fft_acml.c.o CMakeFiles/md.dir/tpi.c.o CMakeFiles/md.dir/ewald.c.o CMakeFiles/md.dir/calcvir.c.o nbnxn_cuda/libnbnxn_cuda.a ../gmxlib/libgmx.so.6 /usr/lib/libblas.so.3gf /usr/lib/liblapack.so.3gf /usr/lib/libblas.so.3gf -ldl -lm -lfftw3f -openmp /usr/lib/liblapack.so.3gf -ldl -lm -lfftw3f ../gmxlib/gpu_utils/libgpu_utils.a ../gmxlib/cuda_tools/libcuda_tools.a /usr/local/cuda/lib64/libcudart.so -lcuda -lpthread -Wl,-rpath,/home/ffavela/Downloads/gromacs-4.6/build-cmake/src/gmxlib:/usr/local/cuda/lib64: cd /home/ffavela/Downloads/gromacs-4.6/build-cmake/src/mdlib /usr/bin/cmake -E cmake_symlink_library libmd.so.6 libmd.so.6 libmd.so make[2]: Leaving directory `/home/ffavela/Downloads/gromacs-4.6/build-cmake' /usr/bin/cmake -E cmake_progress_report /home/ffavela/Downloads/gromacs-4.6/build-cmake/CMakeFiles 89 90 91 92 93 94 95 96 97 [ 65%] Built target md make[1]: Leaving directory `/home/ffavela/Downloads/gromacs-4.6/build-cmake' make: *** [all] Error 2 I think this issue must be related with the compilers because if I use the default gnu compilers the problem disappear. Could anybody help me please? Thanks in advance. Fernando. NOTE: after an eventual successful installation, where can I find information of how to get the benefits of gromacs-gpu? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the
[gmx-users] Re: clarification regarding contact map - g_mdmat
Dear users, Sorry. It is because the unit of the cutoff distance ]is in nm. Thank you kavya On Fri, Feb 1, 2013 at 1:28 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, I used g_mdmap to calculate the C-alpha contact map of the trajectory. the distance cut off of 8.0 Ang was selected The protein is a dimer of 237 residues. The output of -no was like this - #resratio tot mean natm mean/atm 1 1.000 473 473.0001 473.000 2 1.000 473 473.0001 473.000 3 1.000 473 473.0001 473.000 4 1.000 473 473.0001 473.000 5 1.000 473 473.0001 473.000 6 1.000 473 473.0001 473.000 7 1.000 473 473.0001 473.000 So it mean that on an average each calpha atom contacts all other C-alpha atom in the whole trajectory at some point of time. In order to cross check it I collected data only for one time frame. This was also very similar results. all the residues have a minimum of atleast 471 contacts. Some one kindly clarify where I am going wrong.? the command I used was - g_mdmat -f .*.xtc -s *.tpr -no *.xvg -mean *.xpm -b 4000 -e 4000 -t 8.0 Is this trucating distance in Angstroms or nanometer? Thank you Kavya -- 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: MM-GB/SA analysis in Gromacs
Hello dear, I have performed a 50 ns MD simulation of a protein with ligand using gromacs software. I need to do mmpbsa calculation but gromacs don't have this option. I see your paper and your discussion about a script you made to calculate mmpbsa using gromacs trajectory, can you give me access to your mmpbsa tool? my email is: loire...@gmail.com Thank you, best regards David -- View this message in context: http://gromacs.5086.n6.nabble.com/MM-GB-SA-analysis-in-Gromacs-tp5003337p5005077.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] MM-GB/SA analysis in Gromacs
Hi Andrea, Thank you so much for bringing forth the paper. I have performed a MD simulation and would very much like to use the tool mentioned in the paper to calculate the binding free energy. Is it possible for you to kindly give me an access to the same and also a brief explanation as to how to use the same? My email id is ankitanaitha...@gmail.com Best Wishes Ankita On Thu, Nov 29, 2012 at 12:32 PM, andrea spitaleri spitaleri.and...@hsr.it wrote: Dear all, I would like to bring to your attention this paper http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0046902 in which we made a tool to perform MM/PBSA binding free energy calculation in automatic fashion, using torque/pbs parallel system implemented in most clusters. The input of the tools are just the xtc trajectory, the tpr and eventually the index file. It does perform the computational alanine scanning (CAS) too. The tool is available upon request. Further details on the paper. Regards, and On 11/29/2012 10:42 AM, Anna Marabotti wrote: Dear gmx-users, I ran several MD simulations using Gromacs 4.5.4 version, and now I'd need to calculate binding free energies using the MM-GBSA method. I searched through the manual and through the gmx-users archive, but I didn't find a way to do it. I found an old post in which it appeared that in the version 4.5 this possibility would have been available (http://lists.gromacs.org/pipermail/gmx-users/2010-July/052302.html), but it seems to me that this kind of analysis has not been implemented yet. In another more recent post, I see that somebody has used mdrun -rerun in order to perform calculations, but I don't understand the correct procedure to use (apart from the suggestion of using .trr instead of .xtc files in order to avoid errors). Does anyone have suggestions in order to do this analysis with Gromacs trajectories, before I make these calculations with another program? Many thanks in advance and best regards Anna -- - Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Fondazione Centro San Raffaele Centro di Genomica Traslazione e Bioinformatica Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano Italy Tel: 0039-0226434348 Fax: 0039-0226434153 http://sites.google.com/site/andreaspitaleri/ http://www.linkedin.com/in/andreaspitaleri - -- 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 -- Ankita Naithani -- 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] gromacs 4.6 installation error
Dear Mark Abraham, without the sudo, the problem is still there: ... … ... [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/ewald.c.o [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/calcvir.c.o Linking CXX shared library libmd.so [ 65%] Built target md make: *** [all] Error 2 It could be possible that after a previous gromacs installation (removed) there's still a linked library or something? Thanks in advance. Fernando. On Feb 1, 2013, at 2:11 AM, Mark Abraham wrote: On Fri, Feb 1, 2013 at 2:18 AM, Fernando Favela ffav...@fis.cinvestav.mxwrote: Dear Gromacs users, I'm trying to install GMX 4.6 in a 64 Bit Machine with Nvidia GTX 680 cards, I've already installed the intel compilers, cuda 5 and openmpi. I do the following procedure: CC=/opt/intel/bin/icc CXX=/opt/intel/bin/icpc cmake .. then sudo make -j 12 Don't use sudo before make. Consider using sudo before make install, per the installation instructions. There's no error message in the output file you posted. I suspect you might running sudo make, and then make and running into file permissions problems because of it. Remove your whole build directory (which will probably need sudo) and start again. Mark and I get this error: Linking CXX shared library libmd.so cd /home/ffavela/Downloads/gromacs-4.6/build-cmake/src/mdlib /usr/bin/cmake -E cmake_link_script CMakeFiles/md.dir/link.txt --verbose=1 /opt/intel/bin/icpc -fPIC -mavx -Wall -ip -funroll-all-loops -O3 -DNDEBUG -shared -Wl,-soname,libmd.so.6 -o libmd.so.6 CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_gpu_ref.c.o CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_simd_4xn.c.o CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_common.c.o CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_simd_2xnn.c.o CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_ref.c.o CMakeFiles/md.dir/genborn_allvsall.c.o CMakeFiles/md.dir/qm_mopac.c.o CMakeFiles/md.dir/mvxvf.c.o CMakeFiles/md.dir/genborn.c.o CMakeFiles/md.dir/ebin.c.o CMakeFiles/md.dir/csettle.c.o CMakeFiles/md.dir/genborn_allvsall_sse2_single.c.o CMakeFiles/md.dir/pme.c.o CMakeFiles/md.dir/gmx_fft.c.o CMakeFiles/md.dir/force.c.o CMakeFiles/md.dir/qm_gaussian.c.o CMakeFiles/md.dir/qm_orca.c.o CMakeFiles/md.dir/mdatom.c.o CMakeFiles/md.dir/stat.c.o CMakeFiles/md.dir/perf_est.c.o CMakeFiles/md.dir/domdec_network.c.o CMakeFiles/md.dir/pme_pp.c.o CMakeFiles/md.dir/calcmu.c.o CMakeFiles/md.dir/shakef.c.o CMakeFiles/md.dir/fft5d.c.o CMakeFiles/md.dir/tables.c.o CMakeFiles/md.dir/qmmm.c.o CMakeFiles/md.dir/domdec_con.c.o CMakeFiles/md.dir/clincs.c.o CMakeFiles/md.dir/domdec_setup.c.o CMakeFiles/md.dir/gmx_wallcycle.c.o CMakeFiles/md.dir/gmx_fft_fftw3.c.o CMakeFiles/md.dir/partdec.c.o CMakeFiles/md.dir/domdec.c.o CMakeFiles/md.dir/genborn_allvsall_sse2_double.c.o CMakeFiles/md.dir/md_support.c.o CMakeFiles/md.dir/vsite.c.o CMakeFiles/md.dir/groupcoord.c.o CMakeFiles/md.dir/mdebin.c.o CMakeFiles/md.dir/gmx_fft_fftpack.c.o CMakeFiles/md.dir/tgroup.c.o CMakeFiles/md.dir/vcm.c.o CMakeFiles/md.dir/nsgrid.c.o CMakeFiles/md.dir/nbnxn_search.c.o CMakeFiles/md.dir/constr.c.o CMakeFiles/md.dir/shellfc.c.o CMakeFiles/md.dir/iteratedconstraints.c.o CMakeFiles/md.dir/rf_util.c.o CMakeFiles/md.dir/update.c.o CMakeFiles/md.dir/genborn_sse2_double.c.o CMakeFiles/md.dir/forcerec.c.o CMakeFiles/md.dir/nbnxn_atomdata.c.o CMakeFiles/md.dir/genborn_sse2_single.c.o CMakeFiles/md.dir/gmx_fft_mkl.c.o CMakeFiles/md.dir/pull.c.o CMakeFiles/md.dir/domdec_box.c.o CMakeFiles/md.dir/domdec_top.c.o CMakeFiles/md.dir/mdebin_bar.c.o CMakeFiles/md.dir/nlistheuristics.c.o CMakeFiles/md.dir/qm_gamess.c.o CMakeFiles/md.dir/coupling.c.o CMakeFiles/md.dir/adress.c.o CMakeFiles/md.dir/init.c.o CMakeFiles/md.dir/wnblist.c.o CMakeFiles/md.dir/expanded.c.o CMakeFiles/md.dir/wall.c.o CMakeFiles/md.dir/ns.c.o CMakeFiles/md.dir/minimize.c.o CMakeFiles/md.dir/sim_util.c.o CMakeFiles/md.dir/pullutil.c.o CMakeFiles/md.dir/gmx_parallel_3dfft.c.o CMakeFiles/md.dir/edsam.c.o CMakeFiles/md.dir/pull_rotation.c.o CMakeFiles/md.dir/gmx_fft_acml.c.o CMakeFiles/md.dir/tpi.c.o CMakeFiles/md.dir/ewald.c.o CMakeFiles/md.dir/calcvir.c.o nbnxn_cuda/libnbnxn_cuda.a ../gmxlib/libgmx.so.6 /usr/lib/libblas.so.3gf /usr/lib/liblapack.so.3gf /usr/lib/libblas.so.3gf -ldl -lm -lfftw3f -openmp /usr/lib/liblapack.so.3gf -ldl -lm -lfftw3f ../gmxlib/gpu_utils/libgpu_utils.a ../gmxlib/cuda_tools/libcuda_tools.a /usr/local/cuda/lib64/libcudart.so -lcuda -lpthread -Wl,-rpath,/home/ffavela/Downloads/gromacs-4.6/build-cmake/src/gmxlib:/usr/local/cuda/lib64: cd /home/ffavela/Downloads/gromacs-4.6/build-cmake/src/mdlib /usr/bin/cmake -E cmake_symlink_library libmd.so.6 libmd.so.6 libmd.so make[2]: Leaving directory `/home/ffavela/Downloads/gromacs-4.6/build-cmake' /usr/bin/cmake -E cmake_progress_report /home/ffavela/Downloads/gromacs-4.6/build-cmake/CMakeFiles 89 90 91 92 93 94 95 96 97 [ 65%] Built target md make[1]: Leaving directory
Re: [gmx-users] gromacs 4.6 installation error
On 2/1/13 8:35 AM, Fernando Favela wrote: Dear Mark Abraham, without the sudo, the problem is still there: ... … ... [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/ewald.c.o [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/calcvir.c.o Linking CXX shared library libmd.so [ 65%] Built target md make: *** [all] Error 2 It could be possible that after a previous gromacs installation (removed) there's still a linked library or something? Not likely, but you still haven't posted the original error. Error 2 says that somewhere higher up there is an Error 1. We need that information. -Justin Thanks in advance. Fernando. On Feb 1, 2013, at 2:11 AM, Mark Abraham wrote: On Fri, Feb 1, 2013 at 2:18 AM, Fernando Favela ffav...@fis.cinvestav.mxwrote: Dear Gromacs users, I'm trying to install GMX 4.6 in a 64 Bit Machine with Nvidia GTX 680 cards, I've already installed the intel compilers, cuda 5 and openmpi. I do the following procedure: CC=/opt/intel/bin/icc CXX=/opt/intel/bin/icpc cmake .. then sudo make -j 12 Don't use sudo before make. Consider using sudo before make install, per the installation instructions. There's no error message in the output file you posted. I suspect you might running sudo make, and then make and running into file permissions problems because of it. Remove your whole build directory (which will probably need sudo) and start again. Mark and I get this error: Linking CXX shared library libmd.so cd /home/ffavela/Downloads/gromacs-4.6/build-cmake/src/mdlib /usr/bin/cmake -E cmake_link_script CMakeFiles/md.dir/link.txt --verbose=1 /opt/intel/bin/icpc -fPIC -mavx -Wall -ip -funroll-all-loops -O3 -DNDEBUG -shared -Wl,-soname,libmd.so.6 -o libmd.so.6 CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_gpu_ref.c.o CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_simd_4xn.c.o CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_common.c.o CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_simd_2xnn.c.o CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_ref.c.o CMakeFiles/md.dir/genborn_allvsall.c.o CMakeFiles/md.dir/qm_mopac.c.o CMakeFiles/md.dir/mvxvf.c.o CMakeFiles/md.dir/genborn.c.o CMakeFiles/md.dir/ebin.c.o CMakeFiles/md.dir/csettle.c.o CMakeFiles/md.dir/genborn_allvsall_sse2_single.c.o CMakeFiles/md.dir/pme.c.o CMakeFiles/md.dir/gmx_fft.c.o CMakeFiles/md.dir/force.c.o CMakeFiles/md.dir/qm_gaussian.c.o CMakeFiles/md.dir/qm_orca.c.o CMakeFiles/md.dir/mdatom.c.o CMakeFiles/md.dir/stat.c.o CMakeFiles/md.dir/perf_est.c.o CMakeFiles/md.dir/domdec_network.c.o CMakeFiles/md.dir/pme_pp.c.o CMakeFiles/md.dir/calcmu.c.o CMakeFiles/md.dir/shakef.c.o CMakeFiles/md.dir/fft5d.c.o CMakeFiles/md.dir/tables.c.o CMakeFiles/md.dir/qmmm.c.o CMakeFiles/md.dir/domdec_con.c.o CMakeFiles/md.dir/clincs.c.o CMakeFiles/md.dir/domdec_setup.c.o CMakeFiles/md.dir/gmx_wallcycle.c.o CMakeFiles/md.dir/gmx_fft_fftw3.c.o CMakeFiles/md.dir/partdec.c.o CMakeFiles/md.dir/domdec.c.o CMakeFiles/md.dir/genborn_allvsall_sse2_double.c.o CMakeFiles/md.dir/md_support.c.o CMakeFiles/md.dir/vsite.c.o CMakeFiles/md.dir/groupcoord.c.o CMakeFiles/md.dir/mdebin.c.o CMakeFiles/md.dir/gmx_fft_fftpack.c.o CMakeFiles/md.dir/tgroup.c.o CMakeFiles/md.dir/vcm.c.o CMakeFiles/md.dir/nsgrid.c.o CMakeFiles/md.dir/nbnxn_search.c.o CMakeFiles/md.dir/constr.c.o CMakeFiles/md.dir/shellfc.c.o CMakeFiles/md.dir/iteratedconstraints.c.o CMakeFiles/md.dir/rf_util.c.o CMakeFiles/md.dir/update.c.o CMakeFiles/md.dir/genborn_sse2_double.c.o CMakeFiles/md.dir/forcerec.c.o CMakeFiles/md.dir/nbnxn_atomdata.c.o CMakeFiles/md.dir/genborn_sse2_single.c.o CMakeFiles/md.dir/gmx_fft_mkl.c.o CMakeFiles/md.dir/pull.c.o CMakeFiles/md.dir/domdec_box.c.o CMakeFiles/md.dir/domdec_top.c.o CMakeFiles/md.dir/mdebin_bar.c.o CMakeFiles/md.dir/nlistheuristics.c.o CMakeFiles/md.dir/qm_gamess.c.o CMakeFiles/md.dir/coupling.c.o CMakeFiles/md.dir/adress.c.o CMakeFiles/md.dir/init.c.o CMakeFiles/md.dir/wnblist.c.o CMakeFiles/md.dir/expanded.c.o CMakeFiles/md.dir/wall.c.o CMakeFiles/md.dir/ns.c.o CMakeFiles/md.dir/minimize.c.o CMakeFiles/md.dir/sim_util.c.o CMakeFiles/md.dir/pullutil.c.o CMakeFiles/md.dir/gmx_parallel_3dfft.c.o CMakeFiles/md.dir/edsam.c.o CMakeFiles/md.dir/pull_rotation.c.o CMakeFiles/md.dir/gmx_fft_acml.c.o CMakeFiles/md.dir/tpi.c.o CMakeFiles/md.dir/ewald.c.o CMakeFiles/md.dir/calcvir.c.o nbnxn_cuda/libnbnxn_cuda.a ../gmxlib/libgmx.so.6 /usr/lib/libblas.so.3gf /usr/lib/liblapack.so.3gf /usr/lib/libblas.so.3gf -ldl -lm -lfftw3f -openmp /usr/lib/liblapack.so.3gf -ldl -lm -lfftw3f ../gmxlib/gpu_utils/libgpu_utils.a ../gmxlib/cuda_tools/libcuda_tools.a /usr/local/cuda/lib64/libcudart.so -lcuda -lpthread -Wl,-rpath,/home/ffavela/Downloads/gromacs-4.6/build-cmake/src/gmxlib:/usr/local/cuda/lib64: cd /home/ffavela/Downloads/gromacs-4.6/build-cmake/src/mdlib /usr/bin/cmake -E cmake_symlink_library libmd.so.6 libmd.so.6 libmd.so make[2]: Leaving directory `/home/ffavela/Downloads/gromacs-4.6/build-cmake' /usr/bin/cmake -E cmake_progress_report
Re: [gmx-users] gromacs 4.6 installation error
Hi justin, this is the other error message: [ 56%] Building C object src/mdlib/CMakeFiles/md.dir/genborn_allvsall.c.o [ 56%] [ 56%] [ 56%] Building C object src/mdlib/CMakeFiles/md.dir/mvxvf.c.o Building C object src/mdlib/CMakeFiles/md.dir/qm_mopac.c.o Building C object src/mdlib/CMakeFiles/md.dir/csettle.c.o Building C object src/mdlib/CMakeFiles/md.dir/ebin.c.o Building C object src/mdlib/CMakeFiles/md.dir/genborn.c.o [ 56%] Building C object src/mdlib/CMakeFiles/md.dir/genborn_allvsall_sse2_single.c.o ld: warning: libimf.so, needed by ../../src/gmxlib/libgmx.so.6, not found (try using -rpath or -rpath-link) ld: warning: libsvml.so, needed by ../../src/gmxlib/libgmx.so.6, not found (try using -rpath or -rpath-link) ld: warning: libirng.so, needed by ../../src/gmxlib/libgmx.so.6, not found (try using -rpath or -rpath-link) ld: warning: libintlc.so.5, needed by ../../src/gmxlib/libgmx.so.6, not found (try using -rpath or -rpath-link) [ 56%] Building C object src/mdlib/CMakeFiles/md.dir/pme.c.o ld: template: hidden symbol `__intel_cpu_indicator_init' in /opt/intel/composer_xe_2013.1.117/compiler/lib/intel64/libirc.a(cpu_disp.o) is referenced by DSO ld: final link failed: Bad value make[2]: *** [share/template/template] Error 1 make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 make[1]: *** Waiting for unfinished jobs…. then ... [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/ewald.c.o [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/calcvir.c.o Linking CXX shared library libmd.so [ 65%] Built target md make: *** [all] Error 2 That's all. Thanks, Fernando. On Feb 1, 2013, at 7:38 AM, Justin Lemkul wrote: On 2/1/13 8:35 AM, Fernando Favela wrote: Dear Mark Abraham, without the sudo, the problem is still there: ... … ... [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/ewald.c.o [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/calcvir.c.o Linking CXX shared library libmd.so [ 65%] Built target md make: *** [all] Error 2 It could be possible that after a previous gromacs installation (removed) there's still a linked library or something? Not likely, but you still haven't posted the original error. Error 2 says that somewhere higher up there is an Error 1. We need that information. -Justin Thanks in advance. Fernando. On Feb 1, 2013, at 2:11 AM, Mark Abraham wrote: On Fri, Feb 1, 2013 at 2:18 AM, Fernando Favela ffav...@fis.cinvestav.mxwrote: Dear Gromacs users, I'm trying to install GMX 4.6 in a 64 Bit Machine with Nvidia GTX 680 cards, I've already installed the intel compilers, cuda 5 and openmpi. I do the following procedure: CC=/opt/intel/bin/icc CXX=/opt/intel/bin/icpc cmake .. then sudo make -j 12 Don't use sudo before make. Consider using sudo before make install, per the installation instructions. There's no error message in the output file you posted. I suspect you might running sudo make, and then make and running into file permissions problems because of it. Remove your whole build directory (which will probably need sudo) and start again. Mark and I get this error: Linking CXX shared library libmd.so cd /home/ffavela/Downloads/gromacs-4.6/build-cmake/src/mdlib /usr/bin/cmake -E cmake_link_script CMakeFiles/md.dir/link.txt --verbose=1 /opt/intel/bin/icpc -fPIC -mavx -Wall -ip -funroll-all-loops -O3 -DNDEBUG -shared -Wl,-soname,libmd.so.6 -o libmd.so.6 CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_gpu_ref.c.o CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_simd_4xn.c.o CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_common.c.o CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_simd_2xnn.c.o CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_ref.c.o CMakeFiles/md.dir/genborn_allvsall.c.o CMakeFiles/md.dir/qm_mopac.c.o CMakeFiles/md.dir/mvxvf.c.o CMakeFiles/md.dir/genborn.c.o CMakeFiles/md.dir/ebin.c.o CMakeFiles/md.dir/csettle.c.o CMakeFiles/md.dir/genborn_allvsall_sse2_single.c.o CMakeFiles/md.dir/pme.c.o CMakeFiles/md.dir/gmx_fft.c.o CMakeFiles/md.dir/force.c.o CMakeFiles/md.dir/qm_gaussian.c.o CMakeFiles/md.dir/qm_orca.c.o CMakeFiles/md.dir/mdatom.c.o CMakeFiles/md.dir/stat.c.o CMakeFiles/md.dir/perf_est.c.o CMakeFiles/md.dir/domdec_network.c.o CMakeFiles/md.dir/pme_pp.c.o CMakeFiles/md.dir/calcmu.c.o CMakeFiles/md.dir/shakef.c.o CMakeFiles/md.dir/fft5d.c.o CMakeFiles/md.dir/tables.c.o CMakeFiles/md.dir/qmmm.c.o CMakeFiles/md.dir/domdec_con.c.o CMakeFiles/md.dir/clincs.c.o CMakeFiles/md.dir/domdec_setup.c.o CMakeFiles/md.dir/gmx_wallcycle.c.o CMakeFiles/md.dir/gmx_fft_fftw3.c.o CMakeFiles/md.dir/partdec.c.o CMakeFiles/md.dir/domdec.c.o CMakeFiles/md.dir/genborn_allvsall_sse2_double.c.o CMakeFiles/md.dir/md_support.c.o CMakeFiles/md.dir/vsite.c.o CMakeFiles/md.dir/groupcoord.c.o CMakeFiles/md.dir/mdebin.c.o CMakeFiles/md.dir/gmx_fft_fftpack.c.o CMakeFiles/md.dir/tgroup.c.o CMakeFiles/md.dir/vcm.c.o CMakeFiles/md.dir/nsgrid.c.o
[gmx-users] ligand topology error
hi, whenever, i Submit the molecule to ATB ( http://compbio.biosci.uq.edu.au/atb/index.py) FOR BUILDING THE TOPOLOGY OF LIGAND, IT SAYS Your job that was submitted at 2013-02-01 00:56:07 (RNME = _NGD) had at least one error. Specifically, the QM calculation failed. The most likely cause is that either: (1) the geometry was inappropriate; (2) the number of hydrogen atoms or the net charge was inappropriate what should i do this to remove the error? -- 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] gromacs 4.6 installation error
Hi, make sure to run source /opt/intel/bin/iccvars.sh intel64 before compiling. Roland On Fri, Feb 1, 2013 at 9:06 AM, Fernando Favela ffav...@fis.cinvestav.mxwrote: Hi justin, this is the other error message: [ 56%] Building C object src/mdlib/CMakeFiles/md.dir/genborn_allvsall.c.o [ 56%] [ 56%] [ 56%] Building C object src/mdlib/CMakeFiles/md.dir/mvxvf.c.o Building C object src/mdlib/CMakeFiles/md.dir/qm_mopac.c.o Building C object src/mdlib/CMakeFiles/md.dir/csettle.c.o Building C object src/mdlib/CMakeFiles/md.dir/ebin.c.o Building C object src/mdlib/CMakeFiles/md.dir/genborn.c.o [ 56%] Building C object src/mdlib/CMakeFiles/md.dir/genborn_allvsall_sse2_single.c.o ld: warning: libimf.so, needed by ../../src/gmxlib/libgmx.so.6, not found (try using -rpath or -rpath-link) ld: warning: libsvml.so, needed by ../../src/gmxlib/libgmx.so.6, not found (try using -rpath or -rpath-link) ld: warning: libirng.so, needed by ../../src/gmxlib/libgmx.so.6, not found (try using -rpath or -rpath-link) ld: warning: libintlc.so.5, needed by ../../src/gmxlib/libgmx.so.6, not found (try using -rpath or -rpath-link) [ 56%] Building C object src/mdlib/CMakeFiles/md.dir/pme.c.o ld: template: hidden symbol `__intel_cpu_indicator_init' in /opt/intel/composer_xe_2013.1.117/compiler/lib/intel64/libirc.a(cpu_disp.o) is referenced by DSO ld: final link failed: Bad value make[2]: *** [share/template/template] Error 1 make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 make[1]: *** Waiting for unfinished jobs…. then ... [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/ewald.c.o [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/calcvir.c.o Linking CXX shared library libmd.so [ 65%] Built target md make: *** [all] Error 2 That's all. Thanks, Fernando. On Feb 1, 2013, at 7:38 AM, Justin Lemkul wrote: On 2/1/13 8:35 AM, Fernando Favela wrote: Dear Mark Abraham, without the sudo, the problem is still there: ... … ... [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/ewald.c.o [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/calcvir.c.o Linking CXX shared library libmd.so [ 65%] Built target md make: *** [all] Error 2 It could be possible that after a previous gromacs installation (removed) there's still a linked library or something? Not likely, but you still haven't posted the original error. Error 2 says that somewhere higher up there is an Error 1. We need that information. -Justin Thanks in advance. Fernando. On Feb 1, 2013, at 2:11 AM, Mark Abraham wrote: On Fri, Feb 1, 2013 at 2:18 AM, Fernando Favela ffav...@fis.cinvestav.mxwrote: Dear Gromacs users, I'm trying to install GMX 4.6 in a 64 Bit Machine with Nvidia GTX 680 cards, I've already installed the intel compilers, cuda 5 and openmpi. I do the following procedure: CC=/opt/intel/bin/icc CXX=/opt/intel/bin/icpc cmake .. then sudo make -j 12 Don't use sudo before make. Consider using sudo before make install, per the installation instructions. There's no error message in the output file you posted. I suspect you might running sudo make, and then make and running into file permissions problems because of it. Remove your whole build directory (which will probably need sudo) and start again. Mark and I get this error: Linking CXX shared library libmd.so cd /home/ffavela/Downloads/gromacs-4.6/build-cmake/src/mdlib /usr/bin/cmake -E cmake_link_script CMakeFiles/md.dir/link.txt --verbose=1 /opt/intel/bin/icpc -fPIC -mavx -Wall -ip -funroll-all-loops -O3 -DNDEBUG -shared -Wl,-soname,libmd.so.6 -o libmd.so.6 CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_gpu_ref.c.o CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_simd_4xn.c.o CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_common.c.o CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_simd_2xnn.c.o CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_ref.c.o CMakeFiles/md.dir/genborn_allvsall.c.o CMakeFiles/md.dir/qm_mopac.c.o CMakeFiles/md.dir/mvxvf.c.o CMakeFiles/md.dir/genborn.c.o CMakeFiles/md.dir/ebin.c.o CMakeFiles/md.dir/csettle.c.o CMakeFiles/md.dir/genborn_allvsall_sse2_single.c.o CMakeFiles/md.dir/pme.c.o CMakeFiles/md.dir/gmx_fft.c.o CMakeFiles/md.dir/force.c.o CMakeFiles/md.dir/qm_gaussian.c.o CMakeFiles/md.dir/qm_orca.c.o CMakeFiles/md.dir/mdatom.c.o CMakeFiles/md.dir/stat.c.o CMakeFiles/md.dir/perf_est.c.o CMakeFiles/md.dir/domdec_network.c.o CMakeFiles/md.dir/pme_pp.c.o CMakeFiles/md.dir/calcmu.c.o CMakeFiles/md.dir/shakef.c.o CMakeFiles/md.dir/fft5d.c.o CMakeFiles/md.dir/tables.c.o CMakeFiles/md.dir/qmmm.c.o CMakeFiles/md.dir/domdec_con.c.o CMakeFiles/md.dir/clincs.c.o CMakeFiles/md.dir/domdec_setup.c.o CMakeFiles/md.dir/gmx_wallcycle.c.o CMakeFiles/md.dir/gmx_fft_fftw3.c.o CMakeFiles/md.dir/partdec.c.o CMakeFiles/md.dir/domdec.c.o CMakeFiles/md.dir/genborn_allvsall_sse2_double.c.o
Re: [gmx-users] get the center of a cluster using gromacs
Hi, I used this command g_cluster -f input.pdb -s input.pdb -cl output.pdb -nofit -av I got a file containing all the structures of the cluster. I am not sure if the first one is the cluster center? Houcemeddine On Mon, Jan 28, 2013 at 9:49 AM, francesco oteri francesco.ot...@gmail.comwrote: Hi, you can try using g_cluster, taking care to use the option -cl Francesco 2013/1/28 Houcemeddine Othman houce...@gmail.com Hi, How can I get the center of a cluster from a multiple conformers pdb file (a file containing a cluster of a docking poses). I tried to use g_covar to get an average structure but I get a distorted structure when averaging over the whole atoms of the protein. -- 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 -- Cordiali saluti, Dr.Oteri Francesco -- 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 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] Derive the heme charge
Hello, I want to derive the atomic partial charges for heme in chloroperoxidase, since these parameters cannot be found in the GROMOS53a6 force field. Chloroperoxidase is a cysteine-ligated heme protein (high spin) much like P450. In my work, I want to study the interactions between the protein residues of chloroperoxidase and its substrates. Thus, I used the QM software ORCA to optimize the heme-thiolate structure (TPSS/def2-SPVD), and then I used CHELPG method to derive the heme charges. Could anyone tell me if the method I used is suitable for my purpose? In addition, the charges I obtained for Fe (0.931877) and nitrogen (-0.44572, -0.34427, -0.39467, and -0.39467) are largely consistent with two reference. The reference are one in 1995 (Fe: 1.0, N: -0.4; Helms et al. Thermodynamics of water mediating protein-ligand interactions in cytochrome P450cam: a molecular dynamics study, Biophys. J. 69: 810-24) and one in recent (Fe: 0.847, N: -0.37, -0.423, -0.504, and -0.528; Favia et al. (2006) Three-dimensional model of the human aromatase enzyme and density functional parameterization of the iron-containing protoporphyrin IX for a molecular dynamics study of heme-cysteinato cytochromes, Proteins 62: 1073-84). I will greatly appreciate any comment and suggestions. Best Regards, Rui -- 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] ligand topology error
On 2/1/13 9:37 AM, az kalsom wrote: hi, whenever, i Submit the molecule to ATB ( http://compbio.biosci.uq.edu.au/atb/index.py) FOR BUILDING THE TOPOLOGY OF LIGAND, IT SAYS Your job that was submitted at 2013-02-01 00:56:07 (RNME = _NGD) had at least one error. Specifically, the QM calculation failed. The most likely cause is that either: (1) the geometry was inappropriate; (2) the number of hydrogen atoms or the net charge was inappropriate what should i do this to remove the error? Please read my previous reply to this same question. This is not the appropriate forum for such questions. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 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] C instead of CH2 in alkane chain with PRODRG
Dear all, I want to produce a perylene with a connected alkane chain using PRODRG. I draw the molecule using JME, run it through PRODRG. Then some of the polar hydrogens connected to the C rings are missing. But the alkane chains have the correct united atom type (CH2/CH3). Following another post, I then take the PDB file, repost into PRODRG, use the ADDHYD command to add hydrogens to the C ring atoms where I want explicit H's and run it through PRODRG. In the result, the desired H's are there, but the CH2/CH3 of the alkane chain have turned into plain Cs! And there are no explicit hydrogens connected to the alkane chains, either. Any hints how to solve this would be greatly appreciated! Thanks a lot in advance, Stephan-- 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] Error in BlueGene
Hello Ricardo, I tried to decrease the integration time but I got the same error. The system is running fine in my local core. I have two questions: 1) What do you mean by I balance the domain decomposition for the larger number of core? 2) Are you running simulations at Bluegene P at Rice University? Thank you, Cíntia On 30/01/2013 20:48, Ricardo Soares wrote: Hello, before submitting to Bluegene, I always test the system in my local 8 core cpu, and if it works, it will also work in Bluegene, as long as I balance the domain decomposition for the larger number of cores. If your system insists in exploding, even after energy minimization, you could try to decrease the integration timestep (dt) to something lower than 2 fs, maybe to 1fs or, in some cases even 0.5 fs. Did you tried that? Cheers, Ricardo. On Wed, 30 Jan 2013 15:44:53 -0200, Cintia C. Vequi-Suplicy wrote Mark, Thank you for your answer. I did an energy minimization with the file em.mdp (below) and then I did a 40 ns simulation with the same md.mdp I send before. These two steps were done in my local cluster. After that I took the configuration for the simulation in the bluegene and I got these error. I notice that the step that the error occurs depends on the number of nodes I use. I am also including the end of the min.out file. I also tried others integrators for the energy minimization but I always get the same error. Thank you again, Cíntia --- em.mdp integrator = steep tinit= 0.0 dt = 0.002 nsteps = 500 nstcomm = 1 comm-grps= Other SOL nstxout = 100 nstvout = 100 nstfout = 0 nstlog = 100 nstenergy= 100 nstxtcout= 100 xtc_precision= 100 xtc-grps = energygrps = Other SOL nstlist = 5 ns_type = grid pbc = xyz rlist= 1.4 coulombtype = reaction-field rcoulomb = 1.4 epsilon_rf = 66 vdw_type = cut-off rvdw = 1.4 DispCorr = No constraints = none --- min.out ... Step= 5192, Dmax= 1.9e-11 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, atom= 22015 Step= 5193, Dmax= 9.5e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, atom= 22015 Step= 5194, Dmax= 4.7e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, atom= 22015 Step= 5195, Dmax= 2.4e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, atom= 22015 Step= 5196, Dmax= 2.8e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, atom= 22015 Step= 5197, Dmax= 1.4e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, atom= 22015 Step= 5198, Dmax= 1.7e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, atom= 22015 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 5199 steps, but did not reach the requested Fmax 10. Potential Energy = -1.79302464181879e+06 Maximum force = 6.65022934447791e+02 on atom 22015 Norm of force = 4.90065871184878e+00 gcq#0: Thanx for Using GROMACS - Have a Nice Day --- --- md.mdp file integrator = md tinit= 0.0 dt = 0.002 nsteps = 500 nstcomm = 5 comm-grps= Other SOL nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 1000 nstenergy= 1000 nstxtcout= 1000 xtc_precision= 1000 xtc-grps = energygrps = Other SOL nstlist = 5 ns_type = grid pbc = xyz rlist= 1.4 coulombtype = reaction-field rcoulomb = 1.4 epsilon_rf = 66 vdw_type = cut-off rvdw = 1.4 DispCorr = No tcoupl = v-rescale tc-grps = Other SOL tau_t= 0.4 0.4 ref_t= 296 296 Pcoupl = berendsen Pcoupltype = semiisotropic tau_p= 0.2 0.2 compressibility = 4.51e-5 4.51e-5 ref_p
Re: [gmx-users] get the center of a cluster using gromacs
On 2013-02-01 16:14, Houcemeddine Othman wrote: Hi, I used this command g_cluster -f input.pdb -s input.pdb -cl output.pdb -nofit -av I got a file containing all the structures of the cluster. I am not sure if the first one is the cluster center? It says in the cluster.log file. Houcemeddine On Mon, Jan 28, 2013 at 9:49 AM, francesco oteri francesco.ot...@gmail.comwrote: Hi, you can try using g_cluster, taking care to use the option -cl Francesco 2013/1/28 Houcemeddine Othman houce...@gmail.com Hi, How can I get the center of a cluster from a multiple conformers pdb file (a file containing a cluster of a docking poses). I tried to use g_covar to get an average structure but I get a distorted structure when averaging over the whole atoms of the protein. -- 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 -- Cordiali saluti, Dr.Oteri Francesco -- 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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] C instead of CH2 in alkane chain with PRODRG
On 2/1/13 11:47 AM, Stephan Gekle wrote: Dear all, I want to produce a perylene with a connected alkane chain using PRODRG. I draw the molecule using JME, run it through PRODRG. Then some of the polar hydrogens connected to the C rings are missing. But the alkane chains have the correct united atom type (CH2/CH3). Following another post, I then take the PDB file, repost into PRODRG, use the ADDHYD command to add hydrogens to the C ring atoms where I want explicit H's and run it through PRODRG. In the result, the desired H's are there, but the CH2/CH3 of the alkane chain have turned into plain Cs! And there are no explicit hydrogens connected to the alkane chains, either. Any hints how to solve this would be greatly appreciated! Works fine for me using JME. I find that when uploading a .pdb file, all hydrogens should be present. Sometimes I think it misinterprets hybridization state without them. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 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] Dynamics of the salt-bridges
Dear Gromacs users! I have trajectory from which I want to investigate dynamics of all possible salt bridges (E.g distance between adjacent + and - charged residues) of my protein during the simulation As I understood ussage of g_saltbr -t -sep could be suitable for such thing but I'm not sure in validness of -t for definition of the native salt bridges ( e.g with the default settings g_saltbr produced huge number of all possible combinations of the polar contacts within my protein ). Is there any others gromacs tols for such investigation? James -- 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] Dynamics of the salt-bridges
On 2/1/13 3:22 PM, James Starlight wrote: Dear Gromacs users! I have trajectory from which I want to investigate dynamics of all possible salt bridges (E.g distance between adjacent + and - charged residues) of my protein during the simulation As I understood ussage of g_saltbr -t -sep could be suitable for such thing but I'm not sure in validness of -t for definition of the native salt bridges ( e.g with the default settings g_saltbr produced huge number of all possible combinations of the polar contacts within my protein ). Is there any others gromacs tols for such investigation? Not really. If you're looking for any possible combinations of charged residues, g_saltbr is the only way to go. The default value of -t basically means everything is always considered, which you may not want. A more physically relevant truncation distance is probably warranted, but it's been a long time since I've played with it. You can always make subset trajectories (with matching .tpr files from tpbconv) to analyze smaller chunks of residues and ignore things you may not care about, like ions. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 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: question about fftw3 in gromacs 4.6 installation
Hi Justin! I had the same problem and I used your advise but I am not sure if this entirely worked for me... I used: cmake -DGMX_MPI=ON DCMAKE_INSTALL_PREFIX=$HOME/gromacs -DFFTWF_INCLUDE_DIR=$HOME/fftw/include -DFFTWF_LIBRARY=$HOME/fftw/lib/libfftw3f.so -DCMAKE_PREFIX_PATH=$HOME/fftw/ .. and I got: -- checking for module 'fftw3f' -- found fftw3f, version 3.2.2 -- Looking for fftwf_plan_r2r_1d in /home/users/didymos/fftw/lib/libfftw3f.so -- Looking for fftwf_plan_r2r_1d in /home/users/didymos/fftw/lib/libfftw3f.so - found -- Looking for fftwf_have_simd_avx in /home/users/didymos/fftw/lib/libfftw3f.so -- Looking for fftwf_have_simd_avx in /home/users/didymos/fftw/lib/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /home/users/didymos/fftw/lib/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /home/users/didymos/fftw/lib/libfftw3f.so - found So it seems ok but I am not sure about first two lines: -- checking for module 'fftw3f' -- found fftw3f, version 3.2.2 it should be 3.3.3 Thanks a lot! Best! tomek -- View this message in context: http://gromacs.5086.n6.nabble.com/question-about-fftw3-in-gromacs-4-6-installation-tp5004727p5005094.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] BAR histogram results
Hi! I just finished a FE calculation using the BAR method. This is the plot of my histogram.xvg file: http://gromacs.5086.n6.nabble.com/file/n5005095/Screenshot.png It is my understanding that data must be overlaped in order to get adequate sampling (I have been following Justin Lemkul's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/07_analysis.html). However I have a few questions (First two must be really simple, but I just have not been successful): 1. How can I plot the ∂H/∂λ values separately from the ΔH values? I have been trying, but I'm not really an expert using xmgrace. 2. I also tried to plot this data using gnuplot. However, this program does not distinguishes between diferent leyends, as in the xmgrace plot. Is there any way for plotting the this data using this program? 3. Comparing my plot with the one on the tutorial, something is wrong with my sampling. I have been trying to understand Bennett's paper, but I have not been successful. Can someone explain to me the meaning of the values in each axis? How should I interpret this data? What can I do to improve my sampling? Thank you in advance, Sonia Aguilera -- View this message in context: http://gromacs.5086.n6.nabble.com/BAR-histogram-results-tp5005095.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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: question about fftw3 in gromacs 4.6 installation
On 2/1/13 5:26 PM, didymos wrote: Hi Justin! I had the same problem and I used your advise but I am not sure if this entirely worked for me... I used: cmake -DGMX_MPI=ON DCMAKE_INSTALL_PREFIX=$HOME/gromacs -DFFTWF_INCLUDE_DIR=$HOME/fftw/include -DFFTWF_LIBRARY=$HOME/fftw/lib/libfftw3f.so -DCMAKE_PREFIX_PATH=$HOME/fftw/ .. The use of -DCMAKE_PREFIX_PATH eliminates the need for -DFFTWF_INCLUDE_DIR and -DFFTWF_LIBRARY. Not that this is the source of your problem, but you can certainly trim down your command. and I got: -- checking for module 'fftw3f' -- found fftw3f, version 3.2.2 -- Looking for fftwf_plan_r2r_1d in /home/users/didymos/fftw/lib/libfftw3f.so -- Looking for fftwf_plan_r2r_1d in /home/users/didymos/fftw/lib/libfftw3f.so - found -- Looking for fftwf_have_simd_avx in /home/users/didymos/fftw/lib/libfftw3f.so -- Looking for fftwf_have_simd_avx in /home/users/didymos/fftw/lib/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /home/users/didymos/fftw/lib/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /home/users/didymos/fftw/lib/libfftw3f.so - found So it seems ok but I am not sure about first two lines: -- checking for module 'fftw3f' -- found fftw3f, version 3.2.2 it should be 3.3.3 Is there a different FFTW installed anywhere else on your system? I believe the first found fftw3f statement comes from pkgconfig detection, but this is superseded by what you specify manually. Perhaps someone who is more familiar with this element of the build system can comment. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 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] BAR histogram results
On 2/1/13 6:07 PM, Sonia Aguilera wrote: Hi! I just finished a FE calculation using the BAR method. This is the plot of my histogram.xvg file: http://gromacs.5086.n6.nabble.com/file/n5005095/Screenshot.png It is my understanding that data must be overlaped in order to get adequate sampling (I have been following Justin Lemkul's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/07_analysis.html). However I have a few questions (First two must be really simple, but I just have not been successful): 1. How can I plot the ∂H/∂λ values separately from the ΔH values? I have been trying, but I'm not really an expert using xmgrace. You will have to parse the .xvg file, either manually or with a script, in order to separate the data sets. 2. I also tried to plot this data using gnuplot. However, this program does not distinguishes between diferent leyends, as in the xmgrace plot. Is there any way for plotting the this data using this program? All Gromacs programs allow you to turn off XmGrace-specific formatting with -xvg none. 3. Comparing my plot with the one on the tutorial, something is wrong with my sampling. I have been trying to understand Bennett's paper, but I have not been successful. Can someone explain to me the meaning of the values in each axis? How should I interpret this data? What can I do to improve my sampling? In a very basic sense, the result is a series of histograms of energy values from neighboring lambda windows. You need continuity in sampling from lambda = 0 to lambda = 1 in order to establish a reliable value for deltaG. It seems from your plot that you are only using a few lambda points, with large gaps between 0.1, 0.5, and 0.9. You probably need more windows. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 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] Dynamics of the salt-bridges
Justin, I suppose that the ussage of the sub-set of trajectories is suitable when you've already known possible salt-bridge pairs. But that time I'd like to obtain that information from my trajectory. E.g I have membrane-embedded protein which is the buddle of alpha-helixes. I want to examine dynamics of the salt-bridges between helixes first of all ( that interactions might serve as the conformation locks ). For such taks I've tried to use smaller -t distance with g_saltbr (e.g considering dynamics of the residues within 1nm assuming both broken and closed salt-bridges as well as taking into account that my protein is membrane-bound where helixes are situated closely than in water-soluble proteins) but again that produced many wrong pairs. James 2013/2/2 Justin Lemkul jalem...@vt.edu: On 2/1/13 3:22 PM, James Starlight wrote: Dear Gromacs users! I have trajectory from which I want to investigate dynamics of all possible salt bridges (E.g distance between adjacent + and - charged residues) of my protein during the simulation As I understood ussage of g_saltbr -t -sep could be suitable for such thing but I'm not sure in validness of -t for definition of the native salt bridges ( e.g with the default settings g_saltbr produced huge number of all possible combinations of the polar contacts within my protein ). Is there any others gromacs tols for such investigation? Not really. If you're looking for any possible combinations of charged residues, g_saltbr is the only way to go. The default value of -t basically means everything is always considered, which you may not want. A more physically relevant truncation distance is probably warranted, but it's been a long time since I've played with it. You can always make subset trajectories (with matching .tpr files from tpbconv) to analyze smaller chunks of residues and ignore things you may not care about, like ions. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 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 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
