[gmx-users] compiling gromacs4.5 with gpu
Hi, there: I was trying to compile gromacs4.5.1 on a GPU cluster (https://secure.nersc.gov/nusers/systems/dirac/ ). The compilation seems to work fine, but in the installation folder, only bin/mdrun-gpu presents. Is it supposed to be so? When I type ./mdrun-gpu -h, the following error occurs: ./mdrun-gpu: error while loading shared libraries: libgmxpreprocess.so. 6: cannot open shared object file: No such file or directory Do you have any idea what this means? Thanks a lot, Bin = Here are steps I did for compiling: export OPENMM_ROOT_DIR=/global/homes/b/bingo/Program/OpenMM2.0-Linux64 cmake -DGMX_OPENMM=ON -DCMAKE_INSTALL_PREFIX=/global/homes/b/bingo/ Program/gromacs_gpu make mdrun make install-mdrun == Here are the outputs from the cmake -- The C compiler identification is GNU -- The CXX compiler identification is GNU -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- CTest cannot determine repository type. Please set UPDATE_TYPE to 'cvs' or 'svn'. CTest update will not work. -- Performing Test CFLAGS_WARN -- Performing Test CFLAGS_WARN - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Failed -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN -- Performing Test CXXFLAGS_WARN - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Failed -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- No external FFT libraries needed for the OpenMM build, using fftpack! -- Threads not compatible with OpenMM build, disabled! CMake Warning at CMakeLists.txt:183 (message): CPU-based acceleration turned off, OpenMM does not support/need any! -- Looking for include files HAVE_STRING_H -- Looking for include files HAVE_STRING_H - found -- Looking for include files HAVE_MATH_H -- Looking for include files HAVE_MATH_H - found -- Looking for include files HAVE_LIMITS_H -- Looking for include files HAVE_LIMITS_H - found -- Looking for include files HAVE_MEMORY_H -- Looking for include files HAVE_MEMORY_H - found -- Looking for include files HAVE_UNISTD_H -- Looking for include files HAVE_UNISTD_H - found -- Looking for include files HAVE_PWD_H -- Looking for include files HAVE_PWD_H - found -- Looking for include files HAVE_STDINT_H -- Looking for include files HAVE_STDINT_H - found -- Looking for include files HAVE_STDLIB_H -- Looking for include files HAVE_STDLIB_H - found -- Looking for include files HAVE_PTHREAD_H -- Looking for include files HAVE_PTHREAD_H - found -- Looking for include files HAVE_DIRENT_H -- Looking for include files HAVE_DIRENT_H - found -- Looking for include files HAVE_INTTYPES_H -- Looking for include files HAVE_INTTYPES_H - found -- Looking for include files HAVE_REGEX_H -- Looking for include files HAVE_REGEX_H - found -- Looking for include files HAVE_SYS_TYPES_H -- Looking for include files HAVE_SYS_TYPES_H - found -- Looking for include files HAVE_SYS_STAT_H -- Looking for include files HAVE_SYS_STAT_H - found -- Looking for include files HAVE_SYS_TIME_H -- Looking for include files HAVE_SYS_TIME_H - found -- Looking for include files HAVE_RPC_RPC_H -- Looking for include files HAVE_RPC_RPC_H - found -- Looking for include files HAVE_RPC_XDR_H -- Looking for include files HAVE_RPC_XDR_H - found -- Looking for include files HAVE_XMMINTRIN_H -- Looking for include files HAVE_XMMINTRIN_H - found -- Looking for include files HAVE_EMMINTRIN_H -- Looking for include files HAVE_EMMINTRIN_H - found -- Looking for include files HAVE_PMMINTRIN_H -- Looking for include files HAVE_PMMINTRIN_H - not found. -- Looking for include files HAVE_SMMINTRIN_H -- Looking for include files HAVE_SMMINTRIN_H - not found. -- Looking for include files HAVE_IO_H -- Looking for include files HAVE_IO_H - not found. -- Looking for strcasecmp -- Looking for strcasecmp - found -- Looking for strdup -- Looking for strdup - found -- Looking for vprintf -- Looking for vprintf - found -- Looking for memcmp -- Looking for memcmp - found -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - found -- Looking for _aligned_malloc -- Looking for _aligned_malloc - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for isnan -- Looking for isnan - found -- Looking for _isnan -- Looking for _isnan - not found -- Looking for isfinite --
Re: [gmx-users] MPI and dual-core laptop
Hi, if you only want to use the two processors of you laptop you can simple leave away the --enable-mpi flag. Then it will work in parallel using threads. Use mdrun -nt 2 -s ... to specify two threads. If you anyhow want to compile with MPI, take a look at the config.log file (search for 'Cannot compile and link MPI code') to check the actual cause of your problem, probably some library was not found. Carsten On Sep 27, 2010, at 8:42 PM, simon sham wrote: Hi, I wanted to test the GROMACS MPI version in my dual-processors laptop. I have installed openmpi 1.4.2 version. However, when I tried to configure GROMACS 4.5.1 with --enable-mpi option, I got the following configuration problem: checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with mpicc mpicc is in my /usr/local/bin directory. Questions: 1. Can I run GROMACS 4.5.1 in a dual-processor laptop? 2. If yes, how should I configure the software? Thanks in advance for your insight. Best, Simon Sham -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] Reg: Liquid-liquid interface simulation
Hi all Is that any one have liquid-liquid interface simulation (like lysozyme by justin). if so kindly share it through this discussiion forum.it will be of great help for the newusers like me to use gromacs for liquid-liquid interface simulation. Regards Vinoth -- 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] MPI and dual-core laptop
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 09/27/2010 08:42 PM, simon sham wrote: Hi, I wanted to test the GROMACS MPI version in my dual-processors laptop. I have installed openmpi 1.4.2 version. However, when I tried to configure GROMACS 4.5.1 with --enable-mpi option, I got the following configuration problem: checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with mpicc mpicc is in my /usr/local/bin directory. Questions: 1. Can I run GROMACS 4.5.1 in a dual-processor laptop? 2. If yes, how should I configure the software? Thanks in advance for your insight. Best, Simon Sham Hi, it seems the mpicc compiler does not find the necessary libraries to link or doesn't even find the compiler. Check if mpicc is in your path. To include the missing libraries in the GROMACS configuration use the LDFLAGS and CPPFLAGS variables to set the corresponding pathes. CPPFLAGS=-I/usr/local/include LDFLAGS=-L/usr/local/lib ./configure ... If you have to add further include and library directories you have to add a further -I/... and/or -L/... and put the whole expression after the = into quotes, e.g CPPFLAGS=-I/usr/local/lib - -I/home/user/local/fftw3/include and so on. However if you use Gromacs 4.5 I would use and get common with the CMake system, which really works fine and also a GUI is available that allows you to easy set your variables options. /Flo - -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkyhpcYACgkQLpNNBb9GiPm1AgCfWcXsF7zs+fGV2gGFiGgG1H4o tC0AoJRxehKCtgYNSq8qa5fqbEagde8a =YCG5 -END PGP SIGNATURE- -- 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] Reg: Liquid-liquid interface simulation
On 2010-09-28 09.58, vinothkumar mohanakrishnan wrote: Hi all Is that any one have liquid-liquid interface simulation (like lysozyme by justin). if so kindly share it through this discussiion forum.it http://forum.it will be of great help for the newusers like me to use gromacs for liquid-liquid interface simulation. Regards Vinoth We prefer to keep discussions on the mailing list for more direct impact and for archiving purposes. If there are tutorials or howtos on certain topics they can be uploaded to the website. -- 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] MPI and dual-core laptop
Hi, You don't need MPI within one machine. Gromacs 4.5 has a built in thread-mpi library that gets built automatically. Berk Date: Tue, 28 Sep 2010 10:22:30 +0200 From: domm...@icp.uni-stuttgart.de To: gmx-users@gromacs.org Subject: Re: [gmx-users] MPI and dual-core laptop -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 09/27/2010 08:42 PM, simon sham wrote: Hi, I wanted to test the GROMACS MPI version in my dual-processors laptop. I have installed openmpi 1.4.2 version. However, when I tried to configure GROMACS 4.5.1 with --enable-mpi option, I got the following configuration problem: checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with mpicc mpicc is in my /usr/local/bin directory. Questions: 1. Can I run GROMACS 4.5.1 in a dual-processor laptop? 2. If yes, how should I configure the software? Thanks in advance for your insight. Best, Simon Sham Hi, it seems the mpicc compiler does not find the necessary libraries to link or doesn't even find the compiler. Check if mpicc is in your path. To include the missing libraries in the GROMACS configuration use the LDFLAGS and CPPFLAGS variables to set the corresponding pathes. CPPFLAGS=-I/usr/local/include LDFLAGS=-L/usr/local/lib ./configure ... If you have to add further include and library directories you have to add a further -I/... and/or -L/... and put the whole expression after the = into quotes, e.g CPPFLAGS=-I/usr/local/lib - -I/home/user/local/fftw3/include and so on. However if you use Gromacs 4.5 I would use and get common with the CMake system, which really works fine and also a GUI is available that allows you to easy set your variables options. /Flo - -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkyhpcYACgkQLpNNBb9GiPm1AgCfWcXsF7zs+fGV2gGFiGgG1H4o tC0AoJRxehKCtgYNSq8qa5fqbEagde8a =YCG5 -END PGP SIGNATURE- -- 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] g_rdf normalization
Dear fellow Gromacs users Does anyone know how the -surf mol option works? I am trying to calculate the coordination number for a molecule in a slice (xy-plane, delta-z ~ 0.5 nm) of my system. I believe I understand how to do the integration of the RDF function if I use the center-of-mass option (-rdf mol_com), but I am more interested in calculating the coordination number with respect to the molecular surface. I have tried to use the -surf mol option together with -cn , and I get what I expected to get, namely N=2. However, when I import the rdf in Excel and do the integration, I get N=1. I should add that I have seen from the manual that the -surf option means that normalization cannot be used. Hence, in my calculations I do not normalize the integral with V/N. Does anyone have any suggestions? Best regards, Soren -- 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] topology file for two molecules
Hi all I want to run a simulation of one tert-pentane molecule inside one organic cage molecule. I have the topology files for both molecules but obviously I only need one .top file as the input for grompp. What is the most convenient way of having both topologies in one file? Many Thanks Gavin -- 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] g_rdf normalization
Hi, g_rdf -surf mol counts the number of atoms within a distance r from the surface, i.e. the atoms which have a distance of less than r to the closest atom of the molecule. Since the surface can be complex and dynamic, normalization is difficult. Berk From: ch...@nus.edu.sg To: gmx-users@gromacs.org Date: Tue, 28 Sep 2010 16:38:58 +0800 Subject: [gmx-users] g_rdf normalization Dear fellow Gromacs users Does anyone know how the “–surf mol” option works? I am trying to calculate the coordination number for a molecule in a slice (xy-plane, delta-z ~ 0.5 nm) of my system. I believe I understand how to do the integration of the RDF function if I use the center-of-mass option (-rdf mol_com), but I am more interested in calculating the coordination number with respect to the molecular surface. I have tried to use the “–surf mol” option together with “–cn “, and I get what I expected to get, namely N=2. However, when I import the rdf in Excel and do the integration, I get N=1. I should add that I have seen from the manual that the “-surf” option means that normalization cannot be used. Hence, in my calculations I do not normalize the integral with V/N. Does anyone have any suggestions? Best regards, Soren -- 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
Re: [gmx-users] topology file for two molecules
Look up the include file mechanism on the webpage. Mark - Original Message - From: Gavin Melaugh gmelaug...@qub.ac.uk Date: Tuesday, September 28, 2010 19:04 Subject: [gmx-users] topology file for two molecules To: Discussion list for GROMACS users gmx-users@gromacs.org Hi all I want to run a simulation of one tert-pentane molecule inside one organic cage molecule. I have the topology files for both molecules but obviously I only need one .top file as the input for grompp. What is the most convenient way of having both topologies in one file? Many Thanks Gavin -- 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
Re: [gmx-users] topology file for two molecules
Hi Mark. I have looked this up, but I am a little uncertain. Does one of the topologies have to be included within the other as an .itp file. If so do I only define the [defaults directive] in the .top file i.e. I take it I don't include this directive in the .itp file as well. Cheers Gavin Mark Abraham wrote: Look up the include file mechanism on the webpage. Mark - Original Message - From: Gavin Melaugh gmelaug...@qub.ac.uk Date: Tuesday, September 28, 2010 19:04 Subject: [gmx-users] topology file for two molecules To: Discussion list for GROMACS users gmx-users@gromacs.org Hi all I want to run a simulation of one tert-pentane molecule inside one organic cage molecule. I have the topology files for both molecules but obviously I only need one .top file as the input for grompp. What is the most convenient way of having both topologies in one file? Many Thanks Gavin -- 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
Re: [gmx-users] Reg: Liquid-liquid interface simulation
Is there any tutorial for liquid-liquid interface in any of the website?. Regards Vinoth On Tue, Sep 28, 2010 at 2:01 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2010-09-28 09.58, vinothkumar mohanakrishnan wrote: Hi all Is that any one have liquid-liquid interface simulation (like lysozyme by justin). if so kindly share it through this discussiion forum.it http://forum.it will be of great help for the newusers like me to use gromacs for liquid-liquid interface simulation. Regards Vinoth We prefer to keep discussions on the mailing list for more direct impact and for archiving purposes. If there are tutorials or howtos on certain topics they can be uploaded to the website. -- 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 -- 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] Reg: Liquid-liquid interface simulation
vinothkumar mohanakrishnan wrote: Is there any tutorial for liquid-liquid interface in any of the website?. If you can't find it at http://www.gromacs.org/Documentation/Tutorials or with Google, then it probably doesn't exist. -Justin Regards Vinoth On Tue, Sep 28, 2010 at 2:01 PM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2010-09-28 09.58, vinothkumar mohanakrishnan wrote: Hi all Is that any one have liquid-liquid interface simulation (like lysozyme by justin). if so kindly share it through this discussiion forum.it http://forum.it/ http://forum.it http://forum.it/ will be of great help for the newusers like me to use gromacs for liquid-liquid interface simulation. Regards Vinoth We prefer to keep discussions on the mailing list for more direct impact and for archiving purposes. If there are tutorials or howtos on certain topics they can be uploaded to the website. -- 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.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se http://folding.bmc.uu.se/ -- gmx-users mailing listgmx-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 -- 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 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] topology file for two molecules
Gavin Melaugh wrote: Hi Mark. I have looked this up, but I am a little uncertain. Does one of the topologies have to be included within the other as an .itp file. If so No. You #include .itp files to simply add molecules within a .top; it would be very rare to #include an .itp within an .itp (although it can be done). For your case, your .top is simple: #include (force field) #include cage.itp #include pentane.itp [ system ] My system [ molecules ] Cage1 Pentane 1 do I only define the [defaults directive] in the .top file i.e. I take it I don't include this directive in the .itp file as well. The [defaults] directive is provided by whatever force field you #include. If you're using some custom parameters, then it needs to be defined once (and only once) at the top of your .top file. Otherwise, you'll get fatal errors from grompp. -Justin Cheers Gavin Mark Abraham wrote: Look up the include file mechanism on the webpage. Mark - Original Message - From: Gavin Melaugh gmelaug...@qub.ac.uk Date: Tuesday, September 28, 2010 19:04 Subject: [gmx-users] topology file for two molecules To: Discussion list for GROMACS users gmx-users@gromacs.org Hi all I want to run a simulation of one tert-pentane molecule inside one organic cage molecule. I have the topology files for both molecules but obviously I only need one .top file as the input for grompp. What is the most convenient way of having both topologies in one file? Many Thanks Gavin -- 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 -- 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 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] topology file for two molecules
Hi Justin Cheers. I have attached my pentane itp file. The cage itp is formatted the same. In the examples there never seems to be [atom types] included. I have included it. Does it seem O.K? Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Mark. I have looked this up, but I am a little uncertain. Does one of the topologies have to be included within the other as an .itp file. If so No. You #include .itp files to simply add molecules within a .top; it would be very rare to #include an .itp within an .itp (although it can be done). For your case, your .top is simple: #include (force field) #include cage.itp #include pentane.itp [ system ] My system [ molecules ] Cage1 Pentane 1 do I only define the [defaults directive] in the .top file i.e. I take it I don't include this directive in the .itp file as well. The [defaults] directive is provided by whatever force field you #include. If you're using some custom parameters, then it needs to be defined once (and only once) at the top of your .top file. Otherwise, you'll get fatal errors from grompp. -Justin Cheers Gavin Mark Abraham wrote: Look up the include file mechanism on the webpage. Mark - Original Message - From: Gavin Melaugh gmelaug...@qub.ac.uk Date: Tuesday, September 28, 2010 19:04 Subject: [gmx-users] topology file for two molecules To: Discussion list for GROMACS users gmx-users@gromacs.org Hi all I want to run a simulation of one tert-pentane molecule inside one organic cage molecule. I have the topology files for both molecules but obviously I only need one .top file as the input for grompp. What is the most convenient way of having both topologies in one file? Many Thanks Gavin -- 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 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CT 12.011000 -0.18 A 0.35 0.276144 HC 1.008000 0.06 A 0.25 0.125520 ;Molecular level [moleculetype] ; name nrexcl tertpentane 3 [atoms] ; atomnr type resnr residue namecgnr charge mass 1 CT 1PENT CT 1 0. 12.0110 2 CT 1PENT CT 1 -0.1800 12.0110 3 CT 1PENT CT 1 -0.1800 12.0110 4 CT 1PENT CT 1 -0.1800 12.0110 5 CT 1PENT CT 1 -0.1800 12.0110 6 HC 1PENT HC 1 0.0600 1.0080 7 HC 1PENT HC 1 0.0600 1.0080 8 HC 1PENT HC 1 0.0600 1.0080 9 HC 1PENT HC 1 0.0600 1.0080 10 HC 1PENT HC 1 0.0600 1.0080 11 HC 1PENT HC 1 0.0600 1.0080 12 HC 1PENT HC 1 0.0600 1.0080 13 HC 1PENT HC 1 0.0600 1.0080 14 HC 1PENT HC 1 0.0600 1.0080 15 HC 1PENT HC 1 0.0600 1.0080 16 HC 1PENT HC 1 0.0600 1.0080 17 HC 1PENT HC 1 0.0600 1.0080 [bonds] ; aiaj func b0(nm) kb(kjmol-1 nm-2) 1 2 1 0.1529 224262.4 1 3 1 0.1529 224262.4 1 4 1 0.1529 224262.4 1 5 1 0.1529 224262.4 2 6 1 0.1090 284512.0 2 7 1 0.1090 284512.0 2 8 1 0.1090 284512.0 3 9 1 0.1090 284512.0 310 1 0.1090 284512.0 311 1 0.1090 284512.0 412 1 0.1090 284512.0 413 1 0.1090 284512.0 414 1 0.1090 284512.0 515 1 0.1090 284512.0 516 1 0.1090 284512.0 517 1 0.1090 284512.0 [angles] ; aiajak func theta(deg)ktheta(kjmol-1 rad-2) 2 1 3 1 112.70 488.2728 2 1 4 1 112.70 488.2728 2 1 5 1 112.70 488.2728 3 1 4 1 112.70 488.2728 3 1 5 1 112.70 488.2728 4 1 5 1 112.70 488.2728 1 2 6 1 110.70 313.8000 1 2 7 1 110.70 313.8000 1 2 8 1 110.70 313.8000
Re: [gmx-users] topology file for two molecules
Gavin Melaugh wrote: Hi Justin Cheers. I have attached my pentane itp file. The cage itp is formatted the same. In the examples there never seems to be [atom types] included. I have included it. Does it seem O.K? You only need to use an [atomtypes] directive if you're introducing new atom types into the force field. I don't know if it's necessary. I also don't know if these sections can be discontinuous (i.e., one section present in cage.itp, another in tertpentane.itp). Try the approach I sent you and see. If you get fatal errors, then you may have to assemble a single [atomtypes] directive and put it either in the first .itp file you #include, or before any of the #includes in the .top (since #include really just means cut-and-paste the stuff here, it works the same). -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Mark. I have looked this up, but I am a little uncertain. Does one of the topologies have to be included within the other as an .itp file. If so No. You #include .itp files to simply add molecules within a .top; it would be very rare to #include an .itp within an .itp (although it can be done). For your case, your .top is simple: #include (force field) #include cage.itp #include pentane.itp [ system ] My system [ molecules ] Cage1 Pentane 1 do I only define the [defaults directive] in the .top file i.e. I take it I don't include this directive in the .itp file as well. The [defaults] directive is provided by whatever force field you #include. If you're using some custom parameters, then it needs to be defined once (and only once) at the top of your .top file. Otherwise, you'll get fatal errors from grompp. -Justin Cheers Gavin Mark Abraham wrote: Look up the include file mechanism on the webpage. Mark - Original Message - From: Gavin Melaugh gmelaug...@qub.ac.uk Date: Tuesday, September 28, 2010 19:04 Subject: [gmx-users] topology file for two molecules To: Discussion list for GROMACS users gmx-users@gromacs.org Hi all I want to run a simulation of one tert-pentane molecule inside one organic cage molecule. I have the topology files for both molecules but obviously I only need one .top file as the input for grompp. What is the most convenient way of having both topologies in one file? Many Thanks Gavin -- 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 -- 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 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] Reg: Liquid-liquid interface simulation
why don't someone can post the tutorial in the gromacs website? because gromacs was heavily used for liquid-liquid interface simulation.I hope probably i will do it in the near future. Regards Vinoth On Tue, Sep 28, 2010 at 4:05 PM, Justin A. Lemkul jalem...@vt.edu wrote: vinothkumar mohanakrishnan wrote: Is there any tutorial for liquid-liquid interface in any of the website?. If you can't find it at http://www.gromacs.org/Documentation/Tutorials or with Google, then it probably doesn't exist. -Justin Regards Vinoth On Tue, Sep 28, 2010 at 2:01 PM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2010-09-28 09.58, vinothkumar mohanakrishnan wrote: Hi all Is that any one have liquid-liquid interface simulation (like lysozyme by justin). if so kindly share it through this discussiion forum.it http://forum.it/ http://forum.it http://forum.it/ will be of great help for the newusers like me to use gromacs for liquid-liquid interface simulation. Regards Vinoth We prefer to keep discussions on the mailing list for more direct impact and for archiving purposes. If there are tutorials or howtos on certain topics they can be uploaded to the website. -- 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.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se http://folding.bmc.uu.se/ -- gmx-users mailing listgmx-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 -- 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 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
Re: [gmx-users] topology file for two molecules
O.K Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Cheers. I have attached my pentane itp file. The cage itp is formatted the same. In the examples there never seems to be [atom types] included. I have included it. Does it seem O.K? You only need to use an [atomtypes] directive if you're introducing new atom types into the force field. I don't know if it's necessary. I also don't know if these sections can be discontinuous (i.e., one section present in cage.itp, another in tertpentane.itp). Try the approach I sent you and see. If you get fatal errors, then you may have to assemble a single [atomtypes] directive and put it either in the first .itp file you #include, or before any of the #includes in the .top (since #include really just means cut-and-paste the stuff here, it works the same). -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Mark. I have looked this up, but I am a little uncertain. Does one of the topologies have to be included within the other as an .itp file. If so No. You #include .itp files to simply add molecules within a .top; it would be very rare to #include an .itp within an .itp (although it can be done). For your case, your .top is simple: #include (force field) #include cage.itp #include pentane.itp [ system ] My system [ molecules ] Cage1 Pentane 1 do I only define the [defaults directive] in the .top file i.e. I take it I don't include this directive in the .itp file as well. The [defaults] directive is provided by whatever force field you #include. If you're using some custom parameters, then it needs to be defined once (and only once) at the top of your .top file. Otherwise, you'll get fatal errors from grompp. -Justin Cheers Gavin Mark Abraham wrote: Look up the include file mechanism on the webpage. Mark - Original Message - From: Gavin Melaugh gmelaug...@qub.ac.uk Date: Tuesday, September 28, 2010 19:04 Subject: [gmx-users] topology file for two molecules To: Discussion list for GROMACS users gmx-users@gromacs.org Hi all I want to run a simulation of one tert-pentane molecule inside one organic cage molecule. I have the topology files for both molecules but obviously I only need one .top file as the input for grompp. What is the most convenient way of having both topologies in one file? Many Thanks Gavin -- 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
Re: [gmx-users] Salt concentration
Thank you Gonçalo and Dallas for your help. Best Regards Anthony 2010/9/27 Gonçalo C. Justino goncalo.just...@gmail.com: Hi Anthony, You can use the '-conc' tag from genion during file preparation, as per http://manual.gromacs.org/current/online/genion.html. Gonçalo On 27 September 2010 15:32, Anthony Cruz Balberdi anthony.cr...@upr.edu wrote: Dear Users: I am interested in perform a simulation of a protein in different salt concentrations. How I can calculate how much Na+ and Cl- ions to include in the simulation to achieve certain concentration? Could someone point me in the right direction? Is there a software to do this type of calculations? Thanks in advance. Anthony -- gmx-users mailing list gmx-us...@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-us...@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] Grompp Error : Segmentation fault
Dear Gromacs Users and Developers, I'm currently using Gromacs 4.5 on a Fedora 12 i686 to performed my ionic liquid MD simulation using amber 99 force field. I got my topology from topolbuild v 1.3. I successfully minimized both cation and anion separately using cg and steep. Then I include the anion in the cation system using genbox. I got error from grompp like this: -- Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# checking input for internal consistency... processing topology... Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Segmentation fault (core dumped) [a...@neox MD1]$ - Still cant find my answer in the mailing list. Sorry for the large post, but here's my .mdp and .top - title = Conjugated-Gradients Energy Minimization ; Preprocessing cpp = /lib/cpp include = -I../top ; Parameters integrator = cg emtol = 1.0 nsteps = 5000 nstenergy = 100 nstxtcout = 100 xtc_grps = System energygrps = System ; Neighboursearching nstlist = 5 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 constraints = none pbc = xyz - ; Topology from .mol2 file ; topolbuild version 1.3 ; Command line: ; topolbuild -n BMIM_Test3 -ff amber99 -dir $AMBERHOME ; ; The force field files to be included #include amber99.ff/forcefield.itp [ moleculetype ] ; name nrexcl BMIM 3 [ atoms ] ; nrtype resnr residu atom cgnrcharge mass 1 CT 1 BMIM C1 -0.17243 12.01100 ; -0.1724300 2 HC 1 BMIM H1 0.07139 1.00800 ; -0.1010400 3 HC 1 BMIM H1 0.05434 1.00800 ; -0.0467000 4 HC 1 BMIM H1 0.05138 1.00800 ; 0.0046800 5 CT 1 BMIM C2 0.02353 12.01100 ; 0.0282100 6 HC 1 BMIM H2 0.02417 1.00800 ; 0.0523800 7 HC 1 BMIM H2 0.02427 1.00800 ; 0.0766500 8 CT 1 BMIM C3 0.01014 12.01100 ; 0.0867900 9 HC 1 BMIM H3 0.03312 1.00800 ; 0.1199100 10 HC 1 BMIM H3 0.02952 1.00800 ; 0.1494300 11 NA 1 BMIM N4 0.05435 14.00670 ; 0.2037800 12 CC 1 BMIM C4 -0.17380 12.01100 ; 0.0299800 13 H4 1 BMIM H4 0.23709 1.00800 ; 0.2670700 14 NA 1 BMIM N6 0.07275 14.00670 ; 0.3398200 15 CT 1 BMIM C5 -0.07367 12.01100 ; 0.2661500 16 H1 1 BMIM H5 0.10657 1.00800 ; 0.3727200 17 H1 1 BMIM H5 0.09108 1.00800 ; 0.4638000 18 CC 1 BMIM C6 -0.08433 12.01100 ; 0.3794700 19 H4 1 BMIM H6 0.20500 1.00800 ; 0.5844700 20 CR 1 BMIM C7 -0.02624 12.01100 ; 0.5582300 21 H5 1 BMIM H7 0.21862 1.00800 ; 0.7768500 22 CT 1 BMIM C8 -0.18403 12.01100 ; 0.5928200 23 H1 1 BMIM H8 0.13823 1.00800 ; 0.7310500 24 H1 1 BMIM H8 0.13886 1.00800 ; 0.8699100 25 H1 1 BMIM H8 0.13010 1.00800 ; 1.100 ; total molecule charge = 1.100 [ bonds ] ; ai aj funct b0 kb 1 5 1 0.15260 259408. ; C- C 1 2 1 0.10900 284512. ; C- H 1 3 1 0.10900 284512. ; C- H 1 4 1 0.10900 284512. ; C- H 5 8 1 0.15260 259408. ; C- C 5 6 1 0.10900 284511. ; C- H 5 7 1 0.10900 284512. ; C- H 815 1 0.15260 259408. ; C- C 8 9 1 0.10900 284512. ; C- H 810 1 0.10900 284512. ; C- H 1112 1 0.13850 353129. ; N- C 1115 1 0.13850 353129. ; N- C 1120 1 0.13850 353129. ; N- C 1218 1 0.14000 392459. ; C- C 1213 1 0.10800
Re: [gmx-users] topology file for two molecules
Hi Justin I Did the following and it worked. You were right about using one atom types directive. If you don't mind I have another query. In all my topology files to date (one molecule type), I have always listed the atomtypes in the [atomtypes] directive, and used the set up in [defaults] below. Is this all that is required for the calculation of the LJ energies. I have never used a pair list, a pair types directive or a nonbond_params directive. From the output I still get LJ energies but I am slightly confused by all the different options. parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CB 12.011000 0.00 A 0.355000 0.292880 CA 12.011000 -0.115000 A 0.355000 0.292880 HC 1.008000 0.115000 A 0.242000 0.125520 CU 13.019000 0.265000 A 0.35 0.334720 NU 14.007000 -0.597000 A 0.325000 0.711280 CH 13.019000 0.332000 A 0.385000 0.334720 C3 15.035000 0.00 A 0.390500 0.732200 CT 12.011000 -0.18 A 0.35 0.276144 HH 1.008000 0.06 A 0.25 0.125520 #include tertpentane.itp #include methylcage.itp ;System level [system] ;the name of this system cage and pentane [molecules] ; moleculename number tertpentane 1 methylcage 1 Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Cheers. I have attached my pentane itp file. The cage itp is formatted the same. In the examples there never seems to be [atom types] included. I have included it. Does it seem O.K? You only need to use an [atomtypes] directive if you're introducing new atom types into the force field. I don't know if it's necessary. I also don't know if these sections can be discontinuous (i.e., one section present in cage.itp, another in tertpentane.itp). Try the approach I sent you and see. If you get fatal errors, then you may have to assemble a single [atomtypes] directive and put it either in the first .itp file you #include, or before any of the #includes in the .top (since #include really just means cut-and-paste the stuff here, it works the same). -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Mark. I have looked this up, but I am a little uncertain. Does one of the topologies have to be included within the other as an .itp file. If so No. You #include .itp files to simply add molecules within a .top; it would be very rare to #include an .itp within an .itp (although it can be done). For your case, your .top is simple: #include (force field) #include cage.itp #include pentane.itp [ system ] My system [ molecules ] Cage1 Pentane 1 do I only define the [defaults directive] in the .top file i.e. I take it I don't include this directive in the .itp file as well. The [defaults] directive is provided by whatever force field you #include. If you're using some custom parameters, then it needs to be defined once (and only once) at the top of your .top file. Otherwise, you'll get fatal errors from grompp. -Justin Cheers Gavin Mark Abraham wrote: Look up the include file mechanism on the webpage. Mark - Original Message - From: Gavin Melaugh gmelaug...@qub.ac.uk Date: Tuesday, September 28, 2010 19:04 Subject: [gmx-users] topology file for two molecules To: Discussion list for GROMACS users gmx-users@gromacs.org Hi all I want to run a simulation of one tert-pentane molecule inside one organic cage molecule. I have the topology files for both molecules but obviously I only need one .top file as the input for grompp. What is the most convenient way of having both topologies in one file? Many Thanks Gavin -- 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
Re: [gmx-users] Grompp Error : Segmentation fault
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello, I am really curious that amber has support for Room Temperature Ionic liquids ? Can you please provide me a reference how this force field works for this kind of liquids. /Flo On 09/28/2010 03:01 PM, Alep Latep wrote: Dear Gromacs Users and Developers, I'm currently using Gromacs 4.5 on a Fedora 12 i686 to performed my ionic liquid MD simulation using amber 99 force field. I got my topology from topolbuild v 1.3. I successfully minimized both cation and anion separately using cg and steep. Then I include the anion in the cation system using genbox. I got error from grompp like this: -- Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# checking input for internal consistency... processing topology... Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Segmentation fault (core dumped) [a...@neox MD1]$ - Still cant find my answer in the mailing list. Sorry for the large post, but here's my .mdp and .top - title = Conjugated-Gradients Energy Minimization ; Preprocessing cpp = /lib/cpp include = -I../top ; Parameters integrator = cg emtol = 1.0 nsteps = 5000 nstenergy = 100 nstxtcout = 100 xtc_grps = System energygrps = System ; Neighboursearching nstlist = 5 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 constraints = none pbc = xyz - ; Topology from .mol2 file ; topolbuild version 1.3 ; Command line: ; topolbuild -n BMIM_Test3 -ff amber99 -dir $AMBERHOME ; ; The force field files to be included #include amber99.ff/forcefield.itp [ moleculetype ] ; name nrexcl BMIM 3 [ atoms ] ; nrtype resnr residu atom cgnrcharge mass 1 CT 1 BMIM C1 -0.17243 12.01100 ; -0.1724300 2 HC 1 BMIM H1 0.07139 1.00800 ; -0.1010400 3 HC 1 BMIM H1 0.05434 1.00800 ; -0.0467000 4 HC 1 BMIM H1 0.05138 1.00800 ; 0.0046800 5 CT 1 BMIM C2 0.02353 12.01100 ; 0.0282100 6 HC 1 BMIM H2 0.02417 1.00800 ; 0.0523800 7 HC 1 BMIM H2 0.02427 1.00800 ; 0.0766500 8 CT 1 BMIM C3 0.01014 12.01100 ; 0.0867900 9 HC 1 BMIM H3 0.03312 1.00800 ; 0.1199100 10 HC 1 BMIM H3 0.02952 1.00800 ; 0.1494300 11 NA 1 BMIM N4 0.05435 14.00670 ; 0.2037800 12 CC 1 BMIM C4 -0.17380 12.01100 ; 0.0299800 13 H4 1 BMIM H4 0.23709 1.00800 ; 0.2670700 14 NA 1 BMIM N6 0.07275 14.00670 ; 0.3398200 15 CT 1 BMIM C5 -0.07367 12.01100 ; 0.2661500 16 H1 1 BMIM H5 0.10657 1.00800 ; 0.3727200 17 H1 1 BMIM H5 0.09108 1.00800 ; 0.4638000 18 CC 1 BMIM C6 -0.08433 12.01100 ; 0.3794700 19 H4 1 BMIM H6 0.20500 1.00800 ; 0.5844700 20 CR 1 BMIM C7 -0.02624 12.01100 ; 0.5582300 21 H5 1 BMIM H7 0.21862 1.00800 ; 0.7768500 22 CT 1 BMIM C8 -0.18403 12.01100 ; 0.5928200 23 H1 1 BMIM H8 0.13823 1.00800 ; 0.7310500 24 H1 1 BMIM H8 0.13886 1.00800 ; 0.8699100 25 H1 1 BMIM H8 0.13010 1.00800 ; 1.100 ; total molecule charge = 1.100 [ bonds ] ; ai aj funct b0 kb 1 5 1 0.15260 259408. ; C- C 1 2 1 0.10900 284512. ; C- H 1 3 1 0.10900 284512. ; C- H 1 4 1 0.10900 284512. ; C- H 5 8 1 0.15260 259408. ; C- C 5 6 1 0.10900 284511. ; C- H 5 7 1 0.10900 284512. ; C- H 815 1 0.15260 259408.
Re: [gmx-users] Reg: Liquid-liquid interface simulation
vinothkumar mohanakrishnan wrote: why don't someone can post the tutorial in the gromacs website? because The implication from my previous message was that, if you cannot find a tutorial in an obvious place, one does not exist. There is not a tutorial for every task that a user may wish to undertake; such a feat would be impossible. gromacs was heavily used for liquid-liquid interface simulation.I hope probably i will do it in the near future. Just because the software has been used for a specific purpose does not necessitate the existence of a tutorial. People who do the simulations do not always have the time to write up (and subsequently maintain) tutorial materials. If you come up with a tutorial, please post it to the Gromacs site. -Justin Regards Vinoth On Tue, Sep 28, 2010 at 4:05 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: vinothkumar mohanakrishnan wrote: Is there any tutorial for liquid-liquid interface in any of the website?. If you can't find it at http://www.gromacs.org/Documentation/Tutorials or with Google, then it probably doesn't exist. -Justin Regards Vinoth On Tue, Sep 28, 2010 at 2:01 PM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2010-09-28 09.58, vinothkumar mohanakrishnan wrote: Hi all Is that any one have liquid-liquid interface simulation (like lysozyme by justin). if so kindly share it through this discussiion forum.it http://forum.it/ http://forum.it/ http://forum.it http://forum.it/ http://forum.it/ will be of great help for the newusers like me to use gromacs for liquid-liquid interface simulation. Regards Vinoth We prefer to keep discussions on the mailing list for more direct impact and for archiving purposes. If there are tutorials or howtos on certain topics they can be uploaded to the website. -- 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.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se http://folding.bmc.uu.se/ http://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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 -- 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 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] topology file for two molecules
Gavin Melaugh wrote: Hi Justin I Did the following and it worked. You were right about using one atom types directive. If you don't mind I have another query. In all my topology files to date (one molecule type), I have always listed the atomtypes in the [atomtypes] directive, and used the set up in [defaults] below. Is this all that is required for the calculation of the LJ energies. I have never used a pair list, a pair types directive or a nonbond_params directive. From the output I still get LJ energies but I am slightly confused by all the different options. I can't give a better explanation than what is already in the manual, specifically section 5.3.3 ([nonbond_params] and whether or not you need it). Whether or not you need [pairs] depends on the underlying mechanics of the force field you're using. See section 5.3.5. -Justin parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CB 12.011000 0.00 A 0.355000 0.292880 CA 12.011000 -0.115000 A 0.355000 0.292880 HC 1.008000 0.115000 A 0.242000 0.125520 CU 13.019000 0.265000 A 0.35 0.334720 NU 14.007000 -0.597000 A 0.325000 0.711280 CH 13.019000 0.332000 A 0.385000 0.334720 C3 15.035000 0.00 A 0.390500 0.732200 CT 12.011000 -0.18 A 0.35 0.276144 HH 1.008000 0.06 A 0.25 0.125520 #include tertpentane.itp #include methylcage.itp ;System level [system] ;the name of this system cage and pentane [molecules] ; moleculename number tertpentane 1 methylcage 1 Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Cheers. I have attached my pentane itp file. The cage itp is formatted the same. In the examples there never seems to be [atom types] included. I have included it. Does it seem O.K? You only need to use an [atomtypes] directive if you're introducing new atom types into the force field. I don't know if it's necessary. I also don't know if these sections can be discontinuous (i.e., one section present in cage.itp, another in tertpentane.itp). Try the approach I sent you and see. If you get fatal errors, then you may have to assemble a single [atomtypes] directive and put it either in the first .itp file you #include, or before any of the #includes in the .top (since #include really just means cut-and-paste the stuff here, it works the same). -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Mark. I have looked this up, but I am a little uncertain. Does one of the topologies have to be included within the other as an .itp file. If so No. You #include .itp files to simply add molecules within a .top; it would be very rare to #include an .itp within an .itp (although it can be done). For your case, your .top is simple: #include (force field) #include cage.itp #include pentane.itp [ system ] My system [ molecules ] Cage1 Pentane 1 do I only define the [defaults directive] in the .top file i.e. I take it I don't include this directive in the .itp file as well. The [defaults] directive is provided by whatever force field you #include. If you're using some custom parameters, then it needs to be defined once (and only once) at the top of your .top file. Otherwise, you'll get fatal errors from grompp. -Justin Cheers Gavin Mark Abraham wrote: Look up the include file mechanism on the webpage. Mark - Original Message - From: Gavin Melaugh gmelaug...@qub.ac.uk Date: Tuesday, September 28, 2010 19:04 Subject: [gmx-users] topology file for two molecules To: Discussion list for GROMACS users gmx-users@gromacs.org Hi all I want to run a simulation of one tert-pentane molecule inside one organic cage molecule. I have the topology files for both molecules but obviously I only need one .top file as the input for grompp. What is the most convenient way of having both topologies in one file? Many Thanks Gavin -- 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 -- 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 --
Re: [gmx-users] topology file for two molecules
Justin Cheers, I had just posted a more general query prior to you getting back? It is perhaps not as vague. Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin I Did the following and it worked. You were right about using one atom types directive. If you don't mind I have another query. In all my topology files to date (one molecule type), I have always listed the atomtypes in the [atomtypes] directive, and used the set up in [defaults] below. Is this all that is required for the calculation of the LJ energies. I have never used a pair list, a pair types directive or a nonbond_params directive. From the output I still get LJ energies but I am slightly confused by all the different options. I can't give a better explanation than what is already in the manual, specifically section 5.3.3 ([nonbond_params] and whether or not you need it). Whether or not you need [pairs] depends on the underlying mechanics of the force field you're using. See section 5.3.5. -Justin parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CB 12.011000 0.00 A 0.355000 0.292880 CA 12.011000 -0.115000 A 0.355000 0.292880 HC 1.008000 0.115000 A 0.242000 0.125520 CU 13.019000 0.265000 A 0.35 0.334720 NU 14.007000 -0.597000 A 0.325000 0.711280 CH 13.019000 0.332000 A 0.385000 0.334720 C3 15.035000 0.00 A 0.390500 0.732200 CT 12.011000 -0.18 A 0.35 0.276144 HH 1.008000 0.06 A 0.25 0.125520 #include tertpentane.itp #include methylcage.itp ;System level [system] ;the name of this system cage and pentane [molecules] ; moleculename number tertpentane 1 methylcage 1 Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Cheers. I have attached my pentane itp file. The cage itp is formatted the same. In the examples there never seems to be [atom types] included. I have included it. Does it seem O.K? You only need to use an [atomtypes] directive if you're introducing new atom types into the force field. I don't know if it's necessary. I also don't know if these sections can be discontinuous (i.e., one section present in cage.itp, another in tertpentane.itp). Try the approach I sent you and see. If you get fatal errors, then you may have to assemble a single [atomtypes] directive and put it either in the first .itp file you #include, or before any of the #includes in the .top (since #include really just means cut-and-paste the stuff here, it works the same). -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Mark. I have looked this up, but I am a little uncertain. Does one of the topologies have to be included within the other as an .itp file. If so No. You #include .itp files to simply add molecules within a .top; it would be very rare to #include an .itp within an .itp (although it can be done). For your case, your .top is simple: #include (force field) #include cage.itp #include pentane.itp [ system ] My system [ molecules ] Cage1 Pentane 1 do I only define the [defaults directive] in the .top file i.e. I take it I don't include this directive in the .itp file as well. The [defaults] directive is provided by whatever force field you #include. If you're using some custom parameters, then it needs to be defined once (and only once) at the top of your .top file. Otherwise, you'll get fatal errors from grompp. -Justin Cheers Gavin Mark Abraham wrote: Look up the include file mechanism on the webpage. Mark - Original Message - From: Gavin Melaugh gmelaug...@qub.ac.uk Date: Tuesday, September 28, 2010 19:04 Subject: [gmx-users] topology file for two molecules To: Discussion list for GROMACS users gmx-users@gromacs.org Hi all I want to run a simulation of one tert-pentane molecule inside one organic cage molecule. I have the topology files for both molecules but obviously I only need one .top file as the input for grompp. What is the most convenient way of having both topologies in one file? Many Thanks Gavin -- 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
Re: [gmx-users] Hardware-specific crash with 4.5.1
Roland Schulz wrote: On Mon, Sep 27, 2010 at 9:58 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: - Original Message - From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Date: Tuesday, September 28, 2010 11:39 Subject: Re: [gmx-users] Hardware-specific crash with 4.5.1 To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Mark Abraham wrote: - Original Message - From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Date: Tuesday, September 28, 2010 11:11 Subject: Re: [gmx-users] Hardware-specific crash with 4.5.1 To: Gromacs Users' List gmx-users@gromacs.org mailto:gmx-users@gromacs.org Roland Schulz wrote: Justin, I think the interaction kernel is not OK on your PowerPC machine. I assume that from: 1) The force seems to be zero (minimization output). 2) When you use the all-to-all kernel which is not available for the powerpc kernel, it automatically falls back to the C kernel and then it works. Sounds about right. What is the kernel you are using? It should say in the log file. Look for: Configuring single precision IBM Power6- specific Fortran kernels or Testing Altivec/VMX support I'm not finding either in the config.log - weird? You were meant to look in the mdrun.log for runtime confirmation of what kernels GROMACS has decided to use. That seems entirely obvious, now that you mention it :) Conveniently, I find the following in the md.log file from the (failing) autoconf-assembled mdrun: Configuring nonbonded kernels... Configuring standard C nonbonded kernels... Testing Altivec/VMX support... present. Configuring PPC/Altivec nonbonded kernels... The (non)MPI CMake build shows the following: Configuring nonbonded kernels... Configuring standard C nonbonded kernels... So it seems clear to me that autoconf built faulty nonbonded kernels, and CMake didn't. OK, so assuming that PPC/Altivec kernels are supposed to be good for Mac (as they were in 4.0.x, I believe): 1) CMake doesn't detect that it should be using those kernels, and so appears to work, but does an inefficient run. autoconf detects that it should use those kernels, but the mdrun fails for reasons that are not yet clear. You can also look in the config.h whether GMX_POWER6 and/or GMX_PPC_ALTIVEC is set. I suggest you try to compile with one/both of them deactivated and see whether that solves it. This will make it slower too. Thus if this is indeed the problem, you will probably want to figure out why the fastest kernel doesn't work correctly to get good performance. It looks like GMX_PPC_ALTIVEC is set. I suppose I could re- compile with this turned off. This is supposed to be fine for Mac, as I understand. Here's what's even weirder. The problematic version was compiled using the standard autoconf procedure. If I use a CMake-compiled version, the energy minimization runs fine, giving the same results (energy and force) as the two systems I know are good. So I guess there's something wrong with the way autoconf installed Gromacs. Perhaps this isn't of concern since Gromacs will require CMake in subsequent releases, but I figure I should at least report it in case it affects anyone else. If I may tack one more question on here, I'm wondering why my CMake installation doesn't actually appear to be using MPI. I get the right result, but the problem is, I get a .log, .edr, and .trr for every processor that's being used, as if each processor is being given its own job and not distributing the work. Here's how I compiled my MPI mdrun, version 4.5.1: At the start and end of the .log files you should get indicators about how many MPI processes were actually being used. That explains it (sort of). It looks like mdrun thinks it's only being run over 1 node, just several times over, and a bunch of junk that isn't getting written properly: Log file opened on Mon Sep 27 21:36:00 2010 Host: n235 pid: 6857 nodeid: 0 nnodes: 1 The Gromacs distribution was built @TMP_TIME@ by jalem...@sysx2.arc-int.vt.edu mailto:jalem...@sysx2.arc-int.vt.edu [CMAKE] (@TMP_MACHINE@) Frustrating. You can set the GMX_NOOPTIMIZEDKERNELS environment variable with your autoconf build to
Re: [gmx-users] compiling gromacs4.5 with gpu
Hi, yes that is a bug with cmake (see http://bugzilla.gromacs.org/show_bug.cgi?id=549). You can either disable BUILD_SHARED_LIBS and or you can ran make install as a workaround until the bug is fixed. Roland On Tue, Sep 28, 2010 at 3:02 AM, BIN ZHANG zhn...@gmail.com wrote: Hi, there: I was trying to compile gromacs4.5.1 on a GPU cluster ( https://secure.nersc.gov/nusers/systems/dirac/). The compilation seems to work fine, but in the installation folder, only bin/mdrun-gpu presents. Is it supposed to be so? When I type ./mdrun-gpu -h, the following error occurs: ./mdrun-gpu: error while loading shared libraries: libgmxpreprocess.so.6: cannot open shared object file: No such file or directory Do you have any idea what this means? Thanks a lot, Bin = Here are steps I did for compiling: export OPENMM_ROOT_DIR=/global/homes/b/bingo/Program/OpenMM2.0-Linux64 cmake -DGMX_OPENMM=ON -DCMAKE_INSTALL_PREFIX=/global/homes/b/bingo/Program/gromacs_gpu make mdrun make install-mdrun == Here are the outputs from the cmake -- The C compiler identification is GNU -- The CXX compiler identification is GNU -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- CTest cannot determine repository type. Please set UPDATE_TYPE to 'cvs' or 'svn'. CTest update will not work. -- Performing Test CFLAGS_WARN -- Performing Test CFLAGS_WARN - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Failed -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN -- Performing Test CXXFLAGS_WARN - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Failed -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- No external FFT libraries needed for the OpenMM build, using fftpack! -- Threads not compatible with OpenMM build, disabled! CMake Warning at CMakeLists.txt:183 (message): CPU-based acceleration turned off, OpenMM does not support/need any! -- Looking for include files HAVE_STRING_H -- Looking for include files HAVE_STRING_H - found -- Looking for include files HAVE_MATH_H -- Looking for include files HAVE_MATH_H - found -- Looking for include files HAVE_LIMITS_H -- Looking for include files HAVE_LIMITS_H - found -- Looking for include files HAVE_MEMORY_H -- Looking for include files HAVE_MEMORY_H - found -- Looking for include files HAVE_UNISTD_H -- Looking for include files HAVE_UNISTD_H - found -- Looking for include files HAVE_PWD_H -- Looking for include files HAVE_PWD_H - found -- Looking for include files HAVE_STDINT_H -- Looking for include files HAVE_STDINT_H - found -- Looking for include files HAVE_STDLIB_H -- Looking for include files HAVE_STDLIB_H - found -- Looking for include files HAVE_PTHREAD_H -- Looking for include files HAVE_PTHREAD_H - found -- Looking for include files HAVE_DIRENT_H -- Looking for include files HAVE_DIRENT_H - found -- Looking for include files HAVE_INTTYPES_H -- Looking for include files HAVE_INTTYPES_H - found -- Looking for include files HAVE_REGEX_H -- Looking for include files HAVE_REGEX_H - found -- Looking for include files HAVE_SYS_TYPES_H -- Looking for include files HAVE_SYS_TYPES_H - found -- Looking for include files HAVE_SYS_STAT_H -- Looking for include files HAVE_SYS_STAT_H - found -- Looking for include files HAVE_SYS_TIME_H -- Looking for include files HAVE_SYS_TIME_H - found -- Looking for include files HAVE_RPC_RPC_H -- Looking for include files HAVE_RPC_RPC_H - found -- Looking for include files HAVE_RPC_XDR_H -- Looking for include files HAVE_RPC_XDR_H - found -- Looking for include files HAVE_XMMINTRIN_H -- Looking for include files HAVE_XMMINTRIN_H - found -- Looking for include files HAVE_EMMINTRIN_H -- Looking for include files HAVE_EMMINTRIN_H - found -- Looking for include files HAVE_PMMINTRIN_H -- Looking for include files HAVE_PMMINTRIN_H - not found. -- Looking for include files HAVE_SMMINTRIN_H -- Looking for include files HAVE_SMMINTRIN_H - not found. -- Looking for include files HAVE_IO_H -- Looking for include files HAVE_IO_H - not found. -- Looking for strcasecmp -- Looking for strcasecmp - found -- Looking for strdup -- Looking for strdup - found -- Looking for vprintf -- Looking for vprintf - found -- Looking for memcmp -- Looking for memcmp - found -- Looking for
Re: [gmx-users] Grompp Error : Segmentation fault
Roland Schulz wrote: Please make sure that the error exists in the latest version. Either 4.5.1 or if you know how please check the latest GIT version from release-4-5-patches. If you still get the error with the latest version, please file a bugzilla report and attach all required files. My first guess would be that these lines are problematic: ; Include TFO topology #include TFO_amber99.itp The .itp filename should be enclosed in quotes. -Justin On Tue, Sep 28, 2010 at 9:01 AM, Alep Latep m.alif.m.la...@gmail.com mailto:m.alif.m.la...@gmail.com wrote: Dear Gromacs Users and Developers, I'm currently using Gromacs 4.5 on a Fedora 12 i686 to performed my ionic liquid MD simulation using amber 99 force field. I got my topology from topolbuild v 1.3. I successfully minimized both cation and anion separately using cg and steep. Then I include the anion in the cation system using genbox. I got error from grompp like this: -- Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# checking input for internal consistency... processing topology... Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Segmentation fault (core dumped) [a...@neox MD1]$ - Still cant find my answer in the mailing list. Sorry for the large post, but here's my .mdp and .top - title = Conjugated-Gradients Energy Minimization ; Preprocessing cpp = /lib/cpp include = -I../top ; Parameters integrator = cg emtol = 1.0 nsteps = 5000 nstenergy = 100 nstxtcout = 100 xtc_grps = System energygrps = System ; Neighboursearching nstlist = 5 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 constraints = none pbc = xyz - ; Topology from .mol2 file ; topolbuild version 1.3 ; Command line: ; topolbuild -n BMIM_Test3 -ff amber99 -dir $AMBERHOME ; ; The force field files to be included #include amber99.ff/forcefield.itp [ moleculetype ] ; name nrexcl BMIM 3 [ atoms ] ; nrtype resnr residu atom cgnrcharge mass 1 CT 1 BMIM C1 -0.17243 12.01100 ; -0.1724300 2 HC 1 BMIM H1 0.07139 1.00800 ; -0.1010400 3 HC 1 BMIM H1 0.05434 1.00800 ; -0.0467000 4 HC 1 BMIM H1 0.05138 1.00800 ; 0.0046800 5 CT 1 BMIM C2 0.02353 12.01100 ; 0.0282100 6 HC 1 BMIM H2 0.02417 1.00800 ; 0.0523800 7 HC 1 BMIM H2 0.02427 1.00800 ; 0.0766500 8 CT 1 BMIM C3 0.01014 12.01100 ; 0.0867900 9 HC 1 BMIM H3 0.03312 1.00800 ; 0.1199100 10 HC 1 BMIM H3 0.02952 1.00800 ; 0.1494300 11 NA 1 BMIM N4 0.05435 14.00670 ; 0.2037800 12 CC 1 BMIM C4 -0.17380 12.01100 ; 0.0299800 13 H4 1 BMIM H4 0.23709 1.00800 ; 0.2670700 14 NA 1 BMIM N6 0.07275 14.00670 ; 0.3398200 15 CT 1 BMIM C5 -0.07367 12.01100 ; 0.2661500 16 H1 1 BMIM H5 0.10657 1.00800 ; 0.3727200 17 H1 1 BMIM H5 0.09108 1.00800 ; 0.4638000 18 CC 1 BMIM C6 -0.08433 12.01100 ; 0.3794700 19 H4 1 BMIM H6 0.20500 1.00800 ; 0.5844700 20 CR 1 BMIM C7 -0.02624 12.01100 ; 0.5582300 21 H5 1 BMIM H7 0.21862 1.00800 ; 0.7768500 22 CT 1 BMIM C8 -0.18403 12.01100 ; 0.5928200 23 H1 1 BMIM H8 0.13823 1.00800 ; 0.7310500 24 H1 1 BMIM H8 0.13886 1.00800 ; 0.8699100 25 H1 1 BMIM H8 0.13010 1.00800 ;
[gmx-users] Looking for force field for metal oxides
Dear gromacs users, I was planning to study the interaction of a peptide with a zinc oxide ( ZnO) surface. So, I was wondering whether there is any forcefield for metal oxide especially for Zinc Oxide ( ZnO) in literarure that you can suggest that can be used in combination with peptide force-field. Thanks Sanku -- 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: MPI and dual-core laptop
Hi, I was finally able to get my MPI GROMACS running on my laptop. Thanks for all those who have provided invaluable suggestions. Best, Simon Sham --- On Mon, 9/27/10, simon sham ssha...@yahoo.com wrote: From: simon sham ssha...@yahoo.com Subject: MPI and dual-core laptop To: gmx-users@gromacs.org Date: Monday, September 27, 2010, 11:42 AM Hi, I wanted to test the GROMACS MPI version in my dual-processors laptop. I have installed openmpi 1.4.2 version. However, when I tried to configure GROMACS 4.5.1 with --enable-mpi option, I got the following configuration problem: checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with mpicc mpicc is in my /usr/local/bin directory. Questions: 1. Can I run GROMACS 4.5.1 in a dual-processor laptop? 2. If yes, how should I configure the software? Thanks in advance for your insight. Best, Simon Sham -- 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] Fw: g_hbond segmentation fault
-- Found 1048 different hydrogen bonds in trajectory Found 2292 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 2/10915Segmentation fault __ Hi guys, I got the msg like above when I ran g_hbond in version 4.5. Any guess on the problem? Thanks, Yao -- 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] Fw: g_hbond segmentation fault
Yao Yao skrev 2010-09-28 19.25: -- Found 1048 different hydrogen bonds in trajectory Found 2292 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 2/10915Segmentation fault __ Hi guys, I got the msg like above when I ran g_hbond in version 4.5. Any guess on the problem? Thanks, Yao And I replied and asked you what was the command line. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@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] Fw: g_hbond segmentation fault
Hi Erik, Sorry about that, I did not notice it. I used the command line, g_hbond -f test.trr -s test.tpr -ac test.xvg -e 100 -dt 1 Thanks, Yao --- On Tue, 9/28/10, Erik Marklund er...@xray.bmc.uu.se wrote: From: Erik Marklund er...@xray.bmc.uu.se Subject: Re: [gmx-users] Fw: g_hbond segmentation fault To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tuesday, September 28, 2010, 6:22 PM Yao Yao skrev 2010-09-28 19.25: -- Found 1048 different hydrogen bonds in trajectory Found 2292 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 2/10915Segmentation fault __ Hi guys, I got the msg like above when I ran g_hbond in version 4.5. Any guess on the problem? Thanks, Yao And I replied and asked you what was the command line. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.se http://folding.bmc.uu.se/ -Inline Attachment Follows- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] topolbuild cannot open logfile
Hello i am very new to molecular mechanics so please excuse me if my questions are a little naive or stupid.I am trying to minimise a mol2 file with topolbuild1_3 using the following command line arguments from within the topolbuild directory: ./topolbuild -dir /usr/local/gromacs/share/gromacs/top -ff oplsaa -n /Users/bioinformatics/Desktop/zinc_12404782 -purge 0 -move I get the following error: Fatal error.Source code file: topolbuild.c, line: 345Cannot open log file zinc_12404782.log I realise that i will have to go over the parameters again but i was hoping for some sort of output. Does anyone know if it is a problem with the parameters of the input file shown below or some problem with the way in which topolbuild is called ? I am a little unsure how to point to the oplsaa force fields? Thanks Andrew mol2 file: @TRIPOSMOLECULEZINC12404782 36 38 0 0 0SMALLUSER_CHARGES[(3R)-1-(1-naphthyl)pyrrolidin-3-yl]methanamine@TRIPOSATOM 1 C1 4.9121 5.4361 -0.0609 C.ar 1 0 -0.1104 2 C2 3.7311 6.1754 -0.0451 C.ar 1 0 -0.1149 3 C3 2.5180 5.5573 -0.0225 C.ar 1 0 -0.1069 4 C4 2.4527 4.1553 -0.0151 C.ar 1 0 -0.0508 5 C5 3.6528 3.4026 -0.0311 C.ar 1 0 -0.0373 6 C6 4.8869 4.0753 -0.0543 C.ar 1 0 -0.1044 7 C7 3.5890 1.9989 -0.0232 C.ar 1 0 -0.1128 8 C8 2.3798 1.3731 -0.0007 C.ar 1 0 -0.0985 9 C9 1.1942 2.1013 0.0157 C.ar 1 0 -0.1624 10 C10 1.2135 3.4800 0.0087 C.ar 1 0 0.0930 11 N1 0.0208 4.1998 0.0243 N.pl3 1 0 -0.4642 12 C11 -1.1513 3.2890 -0.0264 C.3 1 0 0.0276 13 C12 -2.3059 4.1663 0.5194 C.3 1 0 -0.1388 14 C13 -1.6180 4.9899 1.6322 C.3 1 0 -0.1313 15 H1 -1.7859 4.5266 2.6045 H 1 0 0.1043 16 C14 -0.1188 4.9670 1.2811 C.3 1 0 0.0431 17 C15 -2.1414 6.4276 1.6324 C.3 1 0 0.0042 18 H2 5.8616 5.9505 -0.0790 H 1 0 0.1273 19 H3 3.7785 7.2544 -0.0504 H 1 0 0.1244 20 H4 1.6108 6.1430 -0.0060 H 1 0 0.1264 21 H5 5.8102 3.5153 -0.0664 H 1 0 0.1319 22 H6 4.4986 1.4167 -0.0357 H 1 0 0.1310 23 H7 2.3403 0.2939 0.0049 H 1 0 0.1276 24 H8 0.2481 1.5807 0.0339 H 1 0 0.1299 25 H9 -1.3545 2.9801 -1.0518 H 1 0 0.1004 26 H10 -0.9921 2.4211 0.6135 H 1 0 0.0709 27 H11 -3.0996 3.5449 0.9341 H 1 0 0.0885 28 H12 -2.6948 4.8209 -0.2606 H 1 0 0.0875 29 H13 0.4419 4.4789 2.0783 H 1 0 0.0705 30 H14 0.2477 5.9836 1.1382 H 1 0 0.0961 31 H15 -1.5362 7.0345 2.3058 H 1 0 0.1357 32 H16 -2.0827 6.8358 0.6235 H 1 0 0.1409 33 H17 -3.9079 7.3788 2.0939 H 1 0 0.4420 34 H18 -4.1089 5.8327 1.5151 H 1 0 0.4364 35 N2 -3.5360 6.4306 2.1084 N.4 1 0 -0.6468 36 H19 -3.5649 6.0740 3.0708 H 1 0 0.4397@TRIPOSBOND 1 1 6 ar 2 1 2 ar 3 1 18 1 4 2 3 ar 5 2 19 1 6 3 4 ar 7 3 20 1 8 4 10 ar 9 4 5 ar 10 5 6 ar 11 5 7 ar 12 6 21 1 13 7 8 ar 14 7 22 1 15 8 9 ar 16 8 23 1 17 9 10 ar 18 9 24 1 19 10 11 1 20 11 16 1 21 11 12 1 22 12 13 1 23 12 25 1 24 12 26 1 25 13 14 1 26 13 27 1 27 13 28 1 28 14 15 1 29 14 16 1 30 14 17 1 31 16 29 1 32 16 30 1 33 17 31 1 34 17 32 1 35 17 35 1 36 33 35 1 37 34 35 1 38 35 36 1@TRIPOS -- 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] about pull_init and pull_start
Hi all, I am sorry to ask such a question,may it seems very stupid, but I am very confused about it. pull_init is the reference distance at t=0. the reference distance is the distance between the pull group and the reference group? This is a single value, except for geometry position which uses a vector.If it is a single value,it can be negative or positive? pull_start = yes,add the COM distance of the starting conformation to pull_init. What it means? I have seen from somewhere else :Setting pull_start = yes means that the initial COM distance is the reference distance, and we do not have to define a reference (pull_init1) separately for each configuration. How is the pulling force caculated? My case may be a little special, I want to use pull= umbrella,pull_geometry = distance ,but my pull group is very close to reference group ,the Z coordinate of COM of reference group is 1.81939,1.822 for COM of pull group. I came across a problem :Pull reference distance for group 1 is negative (-0.20) Zhongjin He -- 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] about pull_init and pull_start
zhongjin wrote: Hi all, I am sorry to ask such a question,may it seems very stupid, but I am very confused about it. pull_init is the reference distance at t=0. the reference distance is the distance between the pull group and the reference group? This is a single value, except for geometry position which uses a Yes. vector.If it is a single value,it can be negative or positive? pull_start = By definition, a distance (a scalar quantity) must be positive. yes,add the COM distance of the starting conformation to pull_init. What it means? I have seen from somewhere else :Setting pull_start = yes means that the initial COM distance is the reference distance, and we do not have to define a reference (pull_init1) separately for each configuration. How is the Correct. It's an easy way out. Using pull_start = yes + pull_init1 = 0 means that the initial COM distance (whatever it is) is the reference distance. The equivalent could be accomplished by using pull_start = no + pull_init1 = (COM distance) pulling force caculated? My case may be a little special, I want to use pull= Hooke's Law. umbrella,pull_geometry = distance ,but my pull group is very close to reference group ,the Z coordinate of COM of reference group is 1.81939,1.822 for COM of pull group. I came across a problem :Pull reference distance for group 1 is negative (-0.20) You've answered your own question from above without even asking it on the list. You're getting a negative distance, and hence an error. I don't know what settings you're using, but pull_start = yes + pull_init1 = 0 should (in theory) solve the issue. -Justin Zhongjin He -- 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 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
