[gmx-users] Re: [gmx-developers] Free Energy Calculation
It sounds like there is something wrong with the 'B' topology. Have you tried the 'decoupling' .mdp parameters? They're there specifically for your type of calculations. Sander On Sep 2, 2010, at 04:58 , Emanuel Birru wrote: Hi, I am doing a partition coefficient of solute between 1-Octanol and water using gromacs ffG53a6 force field. Actually I am trying to reproduce Garrido et al’ s paper (J. Chem Theory Comput. 2009). The first thing I have done is to predict the Gibbs free energy of salvation of pentane (my solute) in 1-Octanol by thermodynamics integration method using 16 λ (lambda) values. It works well for λ=0. 0.05, 0.1, 0.2, 0.3, 0.4 and 0.5. The problem has stated at λ=0.6 and it is LINCS error which says as follows: Fatal error: Too many LINCS warnings (1001) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem The atoms that make the problem are pentane atoms. I have put the parameter file that I am using on this link http://hydra.pharm.monash.edu.au/md_project/production.txt Before I run the production simulation I minimized the system well as exactly stated on the paper. After I got the error I have tried to run it again by changing the time step and the soft core value i.e sc_alpha and run three jobs independently 1. With 1fs time step and sc_alpha = 1.51 2. With 2fs time step changing sc_alpha to 0.5 and 3. With 1fs time step and 0.5 sc_alpha The same problem happened for 2 and 3 but 1 works well, but the average dVpot/d λ is not what I expected, its +7. I could not figure it out where exactly the problem is. Thanks in advance for your advise. Cheers, Emanuel -- gmx-developers mailing list gmx-develop...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-developers Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-developers-requ...@gromacs.org. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Please test the new Gromacs-4.5!
Dear users, Gromacs-4.5 is finally out and although all major and critical bugs have been cleared, we are aware that there are probably many small issues still left. We would like to ask all users to go ahead and *heavy* test run the code. For example, * compile on different platforms with different compilers * use different MPI and math libraries * use exclusively the CMake build system. Autoconf **will be removed** after this release! * try all new features o Amber and Charmm forcefields o simulated nucleic acids o implicit solvent simulations o Velocity-Verlet integrators, MTTK pressure control and Nose-Hoover chains o Free energy calculations and g_bar * errors/inconsistencies/typos in the documentation If you find any kind of reproducible problems, even minor ones, please file a *bugzilla report *! We will clear them out as soon as possible. If there is no report, we'll assume there is no bug :) This test run will be important for distribution package maintainers - let us know if you have issues specific to your systems. And one more thing - there is a deadline :) We'll try to fix all reports that are filed in *the next two weeks* (i.e by *Sept. 15*)! After that priority will be given to development work on major code restructuring towards 5.0. We're awaiting your reports! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problem with installing mdrun-gpu in Gromacs-4.5
Dear all, so I downloaded Gromacs-4.5 and tried to compile the gpu-version with cmake version 2.8.0 as stated in the gpu installation instructions as export OPENMM_ROOT_DIR=/usr/local/openmm cmake -DGMX_OPENMM=ON -DCMAKE_INSTALL_PREFIX=$HOME/GROMACS_4.5 make mdrun make install-mdrun But I get a few errors: - -- 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. CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message): CPack license resource file: /home/c_muecksch/gpu_Install_Linux/gromacs-4.5/admin/InstallLicense.txt could not be found. Call Stack (most recent call first): /usr/share/cmake-2.8/Modules/CPack.cmake:707 (cpack_check_file_exists) CMakeLists.txt:40 (include) CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message): CPack readme resource file: /home/c_muecksch/gpu_Install_Linux/gromacs-4.5/admin/InstallInfo.txt could not be found. Call Stack (most recent call first): /usr/share/cmake-2.8/Modules/CPack.cmake:708 (cpack_check_file_exists) CMakeLists.txt:40 (include) CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message): CPack welcome resource file: /home/c_muecksch/gpu_Install_Linux/gromacs-4.5/admin/InstallWelcome.txt could not be found. Call Stack (most recent call first): /usr/share/cmake-2.8/Modules/CPack.cmake:709 (cpack_check_file_exists) CMakeLists.txt:40 (include) -- 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 --
Re: [gmx-users] Problem with installing mdrun-gpu in Gromacs-4.5
Today, I have made similar observations and recorded them in the Bugzilla database here http://bugzilla.gromacs.org/show_bug.cgi?id=539 For now, I do not think cmake works properly. autotools have been fine for me, however. Mark - Original Message - From: Christian Mücksch mueck...@rhrk.uni-kl.de Date: Thursday, September 2, 2010 19:26 Subject: [gmx-users] Problem with installing mdrun-gpu in Gromacs-4.5 To: gmx-users@gromacs.org Dear all, so I downloaded Gromacs-4.5 and tried to compile the gpu-version with cmake version 2.8.0 as stated in the gpu installation instructions as export OPENMM_ROOT_DIR=/usr/local/openmm cmake -DGMX_OPENMM=ON -DCMAKE_INSTALL_PREFIX=$HOME/GROMACS_4.5 make mdrun make install-mdrun But I get a few errors: - -- 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. CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message): CPack license resource file: /home/c_muecksch/gpu_Install_Linux/gromacs- 4.5/admin/InstallLicense.txt could not be found. Call Stack (most recent call first): /usr/share/cmake-2.8/Modules/CPack.cmake:707 (cpack_check_file_exists) CMakeLists.txt:40 (include) CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message): CPack readme resource file: /home/c_muecksch/gpu_Install_Linux/gromacs- 4.5/admin/InstallInfo.txt could not be found. Call Stack (most recent call first): /usr/share/cmake-2.8/Modules/CPack.cmake:708 (cpack_check_file_exists) CMakeLists.txt:40 (include) CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message): CPack welcome resource file: /home/c_muecksch/gpu_Install_Linux/gromacs- 4.5/admin/InstallWelcome.txt could not be found. Call Stack (most recent call first): /usr/share/cmake-2.8/Modules/CPack.cmake:709 (cpack_check_file_exists) CMakeLists.txt:40 (include) -- 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
Re: [gmx-users] Problem with installing mdrun-gpu in Gromacs-4.5
Hi, Yes, cmake is broken:) We forgot to add some of the cmake specific files for distribution (which is created using autoconf). I'll release a 4.5.1 right now. A very short lived 4.5 (RIP) :) Rossen On 9/2/10 11:23 AM, Christian Mücksch wrote: Dear all, so I downloaded Gromacs-4.5 and tried to compile the gpu-version with cmake version 2.8.0 as stated in the gpu installation instructions as export OPENMM_ROOT_DIR=/usr/local/openmm cmake -DGMX_OPENMM=ON -DCMAKE_INSTALL_PREFIX=$HOME/GROMACS_4.5 make mdrun make install-mdrun But I get a few errors: - -- 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. CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message): CPack license resource file: /home/c_muecksch/gpu_Install_Linux/gromacs-4.5/admin/InstallLicense.txt could not be found. Call Stack (most recent call first): /usr/share/cmake-2.8/Modules/CPack.cmake:707 (cpack_check_file_exists) CMakeLists.txt:40 (include) CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message): CPack readme resource file: /home/c_muecksch/gpu_Install_Linux/gromacs-4.5/admin/InstallInfo.txt could not be found. Call Stack (most recent call first): /usr/share/cmake-2.8/Modules/CPack.cmake:708 (cpack_check_file_exists) CMakeLists.txt:40 (include) CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message): CPack welcome resource file: /home/c_muecksch/gpu_Install_Linux/gromacs-4.5/admin/InstallWelcome.txt could not be found. Call Stack (most recent call first): /usr/share/cmake-2.8/Modules/CPack.cmake:709 (cpack_check_file_exists) CMakeLists.txt:40 (include) -- 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
Re: [gmx-users] Problem with installing mdrun-gpu in Gromacs-4.5
On Sep 2, 2010, at 11:42 AM, Rossen Apostolov wrote: Hi, Yes, cmake is broken:) We forgot to add some of the cmake specific files for distribution (which is created using autoconf). I'll release a 4.5.1 right now. Hi Rossen, in ./src/tools/CMakeLists.txt the program gmx_rmsdist.c is doubly listed. Maybe you want to fix that also. It gives a warning only, though. Carsten A very short lived 4.5 (RIP) :) Rossen On 9/2/10 11:23 AM, Christian Mücksch wrote: Dear all, so I downloaded Gromacs-4.5 and tried to compile the gpu-version with cmake version 2.8.0 as stated in the gpu installation instructions as export OPENMM_ROOT_DIR=/usr/local/openmm cmake -DGMX_OPENMM=ON -DCMAKE_INSTALL_PREFIX=$HOME/GROMACS_4.5 make mdrun make install-mdrun But I get a few errors: - -- 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. CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message): CPack license resource file: /home/c_muecksch/gpu_Install_Linux/gromacs-4.5/admin/InstallLicense.txt could not be found. Call Stack (most recent call first): /usr/share/cmake-2.8/Modules/CPack.cmake:707 (cpack_check_file_exists) CMakeLists.txt:40 (include) CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message): CPack readme resource file: /home/c_muecksch/gpu_Install_Linux/gromacs-4.5/admin/InstallInfo.txt could not be found. Call Stack (most recent call first): /usr/share/cmake-2.8/Modules/CPack.cmake:708 (cpack_check_file_exists) CMakeLists.txt:40 (include) CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message): CPack welcome resource file: /home/c_muecksch/gpu_Install_Linux/gromacs-4.5/admin/InstallWelcome.txt could not be found. Call Stack (most recent call first): /usr/share/cmake-2.8/Modules/CPack.cmake:709 (cpack_check_file_exists) CMakeLists.txt:40 (include) -- 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
Re: [gmx-users] Problem with installing mdrun-gpu in Gromacs-4.5
On 9/2/10 11:46 AM, Carsten Kutzner wrote: On Sep 2, 2010, at 11:42 AM, Rossen Apostolov wrote: Hi, Yes, cmake is broken:) We forgot to add some of the cmake specific files for distribution (which is created using autoconf). I'll release a 4.5.1 right now. Hi Rossen, in ./src/tools/CMakeLists.txt the program gmx_rmsdist.c is doubly listed. Maybe you want to fix that also. It gives a warning only, though. Thanks Carsten! I fixed that. Strangely, I was getting a warning about it. Rossen Carsten A very short lived 4.5 (RIP) :) Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Please test the new Gromacs-4.5!
Hi, Some CMake specific files were missing from the distributed tarball and were breaking the build system. I've made a new release, 4.5.1, that has a working CMake support. Nothing has changed for autoconf users. Rossen On 9/2/10 10:51 AM, Rossen Apostolov wrote: Dear users, Gromacs-4.5 is finally out and although all major and critical bugs have been cleared, we are aware that there are probably many small issues still left. We would like to ask all users to go ahead and *heavy* test run the code. For example, * compile on different platforms with different compilers * use different MPI and math libraries * use exclusively the CMake build system. Autoconf **will be removed** after this release! * try all new features o Amber and Charmm forcefields o simulated nucleic acids o implicit solvent simulations o Velocity-Verlet integrators, MTTK pressure control and Nose-Hoover chains o Free energy calculations and g_bar * errors/inconsistencies/typos in the documentation If you find any kind of reproducible problems, even minor ones, please file a *bugzilla report *! We will clear them out as soon as possible. If there is no report, we'll assume there is no bug :) This test run will be important for distribution package maintainers - let us know if you have issues specific to your systems. And one more thing - there is a deadline :) We'll try to fix all reports that are filed in *the next two weeks* (i.e by *Sept. 15*)! After that priority will be given to development work on major code restructuring towards 5.0. We're awaiting your reports! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Help regading Gromacs
Please keep all Gromacs-related correspondence on the gmx-users list. I am not a private help service. I am CC'ing the message there; please continue any discussion via the forum. Creating a lipid bilayer is not a particularly easy task. You can generate a leaflet by replicating the coordinates of one lipid molecule in the x-y plane using genbox, then create the facing leaflet by rotating the existing leaflet using editconf. Concatenate the files and you have yourself a bilayer (which will need extensive equilibration, of course). Adding water is trivial with genbox. -Justin praba vathy wrote: Dear Sir, I want to create a lipid bilayer in which protein is inserted and on the top of insertion i need to put the water molecules and then at the bottom as well. I don't understand that how to place the molecules using Gromacs. Please give suggestions. Regards, Prabha. K -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Please test the new Gromacs-4.5!
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 09/02/2010 12:37 PM, Rossen Apostolov wrote: Hi, Some CMake specific files were missing from the distributed tarball and were breaking the build system. I've made a new release, 4.5.1, that has a working CMake support. Nothing has changed for autoconf users. Rossen On 9/2/10 10:51 AM, Rossen Apostolov wrote: Dear users, Gromacs-4.5 is finally out and although all major and critical bugs have been cleared, we are aware that there are probably many small issues still left. We would like to ask all users to go ahead and *heavy* test run the code. For example, * compile on different platforms with different compilers * use different MPI and math libraries * use exclusively the CMake build system. Autoconf **will be removed** after this release! * try all new features o Amber and Charmm forcefields o simulated nucleic acids o implicit solvent simulations o Velocity-Verlet integrators, MTTK pressure control and Nose-Hoover chains o Free energy calculations and g_bar * errors/inconsistencies/typos in the documentation If you find any kind of reproducible problems, even minor ones, please file a *bugzilla report *! We will clear them out as soon as possible. If there is no report, we'll assume there is no bug :) This test run will be important for distribution package maintainers - let us know if you have issues specific to your systems. And one more thing - there is a deadline :) We'll try to fix all reports that are filed in *the next two weeks* (i.e by *Sept. 15*)! After that priority will be given to development work on major code restructuring towards 5.0. We're awaiting your reports! Hello, when I try to use CMake I get a bunch of warnings when generating the Makefile: WARNING: Target md requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_luck requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_protonate requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_x2top requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target gmxcheck requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target gmxdump requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target gmxpreprocess requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target grompp requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target mdrun requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target pdb2gmx requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target tpbconv requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target do_dssp requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target editconf requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target eneconv requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_anadock requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_anaeig requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_analyze requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_angle requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_bar requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_bond requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_bundle requests linking to directory /home/dommert/local/fftw3/lib. Targets may link
[gmx-users] (no subject)
Dear Sir, We have chosen force field Gromos96 53A6 parameter set. In that forcefield, how we add this CA atom type. Prabha -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] (no subject)
Hi Prabha, Why did you choose that force field, and what CA atom type? Tsjerk On Thu, Sep 2, 2010 at 1:30 PM, praba vathy sumipraba2...@gmail.com wrote: Dear Sir, We have chosen force field Gromos96 53A6 parameter set. In that forcefield, how we add this CA atom type. Prabha -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology / University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Please test the new Gromacs-4.5!
Hi Florian, What options did you give to cmake? You have to specify the library name in FFTW3_LIBRARIES, not the lib directory. E.g. $ cmake ../gromacs-4.5.1 -DFFTW3F_LIBRARIES=/home/dommert/local/fftw3/lib/libfftw3f.so Rossen On 9/2/10 1:21 PM, Florian Dommert wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 09/02/2010 12:37 PM, Rossen Apostolov wrote: Hi, Some CMake specific files were missing from the distributed tarball and were breaking the build system. I've made a new release, 4.5.1, that has a working CMake support. Nothing has changed for autoconf users. Rossen On 9/2/10 10:51 AM, Rossen Apostolov wrote: Dear users, Gromacs-4.5 is finally out and although all major and critical bugs have been cleared, we are aware that there are probably many small issues still left. We would like to ask all users to go ahead and *heavy* test run the code. For example, * compile on different platforms with different compilers * use different MPI and math libraries * use exclusively the CMake build system. Autoconf **will be removed** after this release! * try all new features o Amber and Charmm forcefields o simulated nucleic acids o implicit solvent simulations o Velocity-Verlet integrators, MTTK pressure control and Nose-Hoover chains o Free energy calculations and g_bar * errors/inconsistencies/typos in the documentation If you find any kind of reproducible problems, even minor ones, please file a *bugzilla report *! We will clear them out as soon as possible. If there is no report, we'll assume there is no bug :) This test run will be important for distribution package maintainers - let us know if you have issues specific to your systems. And one more thing - there is a deadline :) We'll try to fix all reports that are filed in *the next two weeks* (i.e by *Sept. 15*)! After that priority will be given to development work on major code restructuring towards 5.0. We're awaiting your reports! Hello, when I try to use CMake I get a bunch of warnings when generating the Makefile: WARNING: Target md requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_luck requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_protonate requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_x2top requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target gmxcheck requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target gmxdump requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target gmxpreprocess requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target grompp requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target mdrun requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target pdb2gmx requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target tpbconv requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target do_dssp requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target editconf requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target eneconv requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_anadock requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_anaeig requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_analyze requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_angle requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_bar requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the
Re: [gmx-users] (no subject)
This is probably not intended for the list; it pertains directly to my membrane tutorial and is likely a result of choosing the force field incorrectly or not properly incorporating the lipid parameters as instructed. -Justin Tsjerk Wassenaar wrote: Hi Prabha, Why did you choose that force field, and what CA atom type? Tsjerk On Thu, Sep 2, 2010 at 1:30 PM, praba vathy sumipraba2...@gmail.com wrote: Dear Sir, We have chosen force field Gromos96 53A6 parameter set. In that forcefield, how we add this CA atom type. Prabha -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Please test the new Gromacs-4.5!
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 09/02/2010 01:45 PM, Rossen Apostolov wrote: Hi Florian, What options did you give to cmake? You have to specify the library name in FFTW3_LIBRARIES, not the lib directory. E.g. $ cmake ../gromacs-4.5.1 -DFFTW3F_LIBRARIES=/home/dommert/local/fftw3/lib/libfftw3f.so Hi Rossen, thanks for this very helpful information. Compilation works fine now. However when I try to install with make install I get following error message: CMake Error at share/cmake_install.cmake:40 (FILE): file INSTALL cannot find /home/dommert/Downloads/gromacs-4.5.1/share/template/CMakeLists.txt.template. Call Stack (most recent call first): cmake_install.cmake:37 (INCLUDE) /Flo Rossen On 9/2/10 1:21 PM, Florian Dommert wrote: On 09/02/2010 12:37 PM, Rossen Apostolov wrote: Hi, Some CMake specific files were missing from the distributed tarball and were breaking the build system. I've made a new release, 4.5.1, that has a working CMake support. Nothing has changed for autoconf users. Rossen On 9/2/10 10:51 AM, Rossen Apostolov wrote: Dear users, Gromacs-4.5 is finally out and although all major and critical bugs have been cleared, we are aware that there are probably many small issues still left. We would like to ask all users to go ahead and *heavy* test run the code. For example, * compile on different platforms with different compilers * use different MPI and math libraries * use exclusively the CMake build system. Autoconf **will be removed** after this release! * try all new features o Amber and Charmm forcefields o simulated nucleic acids o implicit solvent simulations o Velocity-Verlet integrators, MTTK pressure control and Nose-Hoover chains o Free energy calculations and g_bar * errors/inconsistencies/typos in the documentation If you find any kind of reproducible problems, even minor ones, please file a *bugzilla report *! We will clear them out as soon as possible. If there is no report, we'll assume there is no bug :) This test run will be important for distribution package maintainers - let us know if you have issues specific to your systems. And one more thing - there is a deadline :) We'll try to fix all reports that are filed in *the next two weeks* (i.e by *Sept. 15*)! After that priority will be given to development work on major code restructuring towards 5.0. We're awaiting your reports! Hello, when I try to use CMake I get a bunch of warnings when generating the Makefile: WARNING: Target md requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_luck requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_protonate requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_x2top requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target gmxcheck requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target gmxdump requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target gmxpreprocess requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target grompp requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target mdrun requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target pdb2gmx requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target tpbconv requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target do_dssp requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target editconf requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target eneconv requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_anadock requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_anaeig requests linking to
Re: [gmx-users] Please test the new Gromacs-4.5!
Hi Florian, Thanks a lot! That was another miss. I have re-packaged 4.5.1 :) So if someone has downloaded it in the last couple of hours, please re-download it again (I know it's not the right thing to do with releases though :-) ) Rossen Hi Rossen, thanks for this very helpful information. Compilation works fine now. However when I try to install with make install I get following error message: CMake Error at share/cmake_install.cmake:40 (FILE): file INSTALL cannot find /home/dommert/Downloads/gromacs-4.5.1/share/template/CMakeLists.txt.template. Call Stack (most recent call first): cmake_install.cmake:37 (INCLUDE) /Flo -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] incomplete frame
Hi everyone, I concatenated many trajectories with trjcat and didn't have any problem. But when I did trjconv, I had this warning: WARNING: Incomplete frame: nr 6077 time 12154 so I tried to do gmxcheck on my concatenated .xtc and got : Reading frame 0 time0.000 # Atoms 192409 Precision 0.001 (nm) Reading frame6000 time 12000.001 WARNING: Incomplete frame: nr 6077 time 12154 Item#frames Timestep (ps) Step 60772 Time 60772 Lambda 0 Coords60772 Velocities 0 Forces 0 Box 60772 please can anyone tell me what might be the problem, knowing that when I gmxcheck the file .xtc that contains this frame, I don't get a warning. Thank you, Carla -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Need help!!!
Hi, I am using simulation for a membrane protein. So i have downloaded the dppc.pdb along with it's topology files. I have used the following steps for the simulation (Based on the link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/01_pdb2gmx.html ). We have used the commands and steps as described in the above link. But we have got a fatal error (Atom type C not found) while running this command, grompp -f mini.mdp -c dppc128.gro -p topol_dppc.top -o em.tp I cant sort out this problem. Please anybody help me to sort out this problem. Awaiting for your valuable replies. Praba -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] incomplete frame
Carla Jamous wrote: Hi everyone, I concatenated many trajectories with trjcat and didn't have any problem. But when I did trjconv, I had this warning: WARNING: Incomplete frame: nr 6077 time 12154 so I tried to do gmxcheck on my concatenated .xtc and got : Reading frame 0 time0.000 # Atoms 192409 Precision 0.001 (nm) Reading frame6000 time 12000.001 WARNING: Incomplete frame: nr 6077 time 12154 Item#frames Timestep (ps) Step 60772 Time 60772 Lambda 0 Coords60772 Velocities 0 Forces 0 Box 60772 please can anyone tell me what might be the problem, knowing that when I gmxcheck the file .xtc that contains this frame, I don't get a warning. Two possibilities: 1. trjcat corrupted the frame when trying to write the full trajectory 2. The original non-concatenated trajectory is corrupted and trjcat passed over the problem, while trjconv cannot. Check the original (non-concatenated) trajectories to assess their integrity. If #1 is true, run trjcat again. If #2 is true, you cannot use the corrupted frame(s), which may mean re-running from a point prior to the corruption. -Justin Thank you, Carla -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Need help!!!
Make sure your gromacs is the latest version. If not, update and try again. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of praba vathy [sumipraba2...@gmail.com] Sent: Thursday, September 02, 2010 9:06 PM To: gmx-users@gromacs.org Subject: [gmx-users] Need help!!! Hi, I am using simulation for a membrane protein. So i have downloaded the dppc.pdb along with it's topology files. I have used the following steps for the simulation (Based on the link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/01_pdb2gmx.html). We have used the commands and steps as described in the above link. But we have got a fatal error (Atom type C not found) while running this command, grompp -f mini.mdp -c dppc128.gro -p topol_dppc.top -o em.tphttp://em.tp I cant sort out this problem. Please anybody help me to sort out this problem. Awaiting for your valuable replies. Praba -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Need help!!!
praba vathy wrote: Hi, I am using simulation for a membrane protein. So i have downloaded the dppc.pdb along with it's topology files. I have used the following steps for the simulation (Based on the link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/01_pdb2gmx.html). We have used the commands and steps as described in the above link. But we have got a fatal error (Atom type C not found) while running this command, grompp -f mini.mdp -c dppc128.gro -p topol_dppc.top -o em.tp http://em.tp I cant sort out this problem. Please anybody help me to sort out this problem. Awaiting for your valuable replies. This is a very different error than what you reported before, and since dppc.itp does not contain atom type C the error indicates (once again) that you have incorrectly constructed the ffG53a6nb_lipid.itp file that is described in the tutorial. Please start over and follow the instructions closely. If you do so, you will not get errors about missing atom types. -Justin Praba -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Need help!!!
#ZHAO LINA# wrote: Make sure your gromacs is the latest version. If not, update and try again. The tutorial is specifically written for version 4.0.5, but will be compatible with any version 4.5. Since the re-organization of the force field directories, the information provided in the tutorial is not correct. I would recommend not upgrading until the OP has sorted out the problem and can then (maybe) work out the appropriate translation to the version 4.5.x scheme. -Justin *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of praba vathy [sumipraba2...@gmail.com] *Sent:* Thursday, September 02, 2010 9:06 PM *To:* gmx-users@gromacs.org *Subject:* [gmx-users] Need help!!! Hi, I am using simulation for a membrane protein. So i have downloaded the dppc.pdb along with it's topology files. I have used the following steps for the simulation (Based on the link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/01_pdb2gmx.html). We have used the commands and steps as described in the above link. But we have got a fatal error (Atom type C not found) while running this command, grompp -f mini.mdp -c dppc128.gro -p topol_dppc.top -o em.tp http://em.tp I cant sort out this problem. Please anybody help me to sort out this problem. Awaiting for your valuable replies. Praba -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Please test the new Gromacs-4.5!
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 09/02/2010 02:56 PM, Rossen Apostolov wrote: Hi Florian, Thanks a lot! That was another miss. I have re-packaged 4.5.1 :) So if someone has downloaded it in the last couple of hours, please re-download it again (I know it's not the right thing to do with releases though :-) ) Rossen Hi, I downloaded the source again from www.gromacs.org, but unfortunately the same error messages occur, while building works fine. Only the share directory is created and then the installation process stops. /Flo Hi Rossen, thanks for this very helpful information. Compilation works fine now. However when I try to install with make install I get following error message: CMake Error at share/cmake_install.cmake:40 (FILE): file INSTALL cannot find /home/dommert/Downloads/gromacs-4.5.1/share/template/CMakeLists.txt.template. Call Stack (most recent call first): cmake_install.cmake:37 (INCLUDE) /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/ iEYEARECAAYFAkx/pOUACgkQLpNNBb9GiPkzHgCgs72naoKbpzjNBGWYWhAds6F+ ZyAAmgKf8RDQG39PIEoNIBfX+V7Z3ySS =zTj+ -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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Need help!!!
But it's a bit trivial to modify those things if you just following those steps by steps. Using the latest version can save lots of works. By the way, thanks for the website, I once followed that too (nearly step by step also). Thanks with best regards, lina P.S actually you can upgrade your website also. ^_^ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Thursday, September 02, 2010 9:12 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Need help!!! #ZHAO LINA# wrote: Make sure your gromacs is the latest version. If not, update and try again. The tutorial is specifically written for version 4.0.5, but will be compatible with any version 4.5. Since the re-organization of the force field directories, the information provided in the tutorial is not correct. I would recommend not upgrading until the OP has sorted out the problem and can then (maybe) work out the appropriate translation to the version 4.5.x scheme. -Justin *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of praba vathy [sumipraba2...@gmail.com] *Sent:* Thursday, September 02, 2010 9:06 PM *To:* gmx-users@gromacs.org *Subject:* [gmx-users] Need help!!! Hi, I am using simulation for a membrane protein. So i have downloaded the dppc.pdb along with it's topology files. I have used the following steps for the simulation (Based on the link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/01_pdb2gmx.html). We have used the commands and steps as described in the above link. But we have got a fatal error (Atom type C not found) while running this command, grompp -f mini.mdp -c dppc128.gro -p topol_dppc.top -o em.tp http://em.tp I cant sort out this problem. Please anybody help me to sort out this problem. Awaiting for your valuable replies. Praba -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Please test the new Gromacs-4.5!
On 9/2/10 3:21 PM, Florian Dommert wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 09/02/2010 02:56 PM, Rossen Apostolov wrote: Hi Florian, Thanks a lot! That was another miss. I have re-packaged 4.5.1 :) So if someone has downloaded it in the last couple of hours, please re-download it again (I know it's not the right thing to do with releases though :-) ) Rossen Hi, I downloaded the source again from www.gromacs.org, but unfortunately the same error messages occur, while building works fine. Only the share directory is created and then the installation process stops. Sorry, can you try downloading again:) Rossen /Flo Hi Rossen, thanks for this very helpful information. Compilation works fine now. However when I try to install with make install I get following error message: CMake Error at share/cmake_install.cmake:40 (FILE): file INSTALL cannot find /home/dommert/Downloads/gromacs-4.5.1/share/template/CMakeLists.txt.template. Call Stack (most recent call first): cmake_install.cmake:37 (INCLUDE) /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/ iEYEARECAAYFAkx/pOUACgkQLpNNBb9GiPkzHgCgs72naoKbpzjNBGWYWhAds6F+ ZyAAmgKf8RDQG39PIEoNIBfX+V7Z3ySS =zTj+ -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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Please test the new Gromacs-4.5!
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 09/02/2010 03:39 PM, Rossen Apostolov wrote: On 9/2/10 3:21 PM, Florian Dommert wrote: On 09/02/2010 02:56 PM, Rossen Apostolov wrote: Hi Florian, Thanks a lot! That was another miss. I have re-packaged 4.5.1 :) So if someone has downloaded it in the last couple of hours, please re-download it again (I know it's not the right thing to do with releases though :-) ) Rossen Hi, I downloaded the source again from www.gromacs.org, but unfortunately the same error messages occur, while building works fine. Only the share directory is created and then the installation process stops. Sorry, can you try downloading again:) Thanks Rossen, everything works fine now with CMake :) Compilation gives just 4 warnings for g_hbond due to uninitialized variables. /Flo Rossen /Flo Hi Rossen, thanks for this very helpful information. Compilation works fine now. However when I try to install with make install I get following error message: CMake Error at share/cmake_install.cmake:40 (FILE): file INSTALL cannot find /home/dommert/Downloads/gromacs-4.5.1/share/template/CMakeLists.txt.template. Call Stack (most recent call first): cmake_install.cmake:37 (INCLUDE) /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 - -- 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/ iEYEARECAAYFAkx/quoACgkQLpNNBb9GiPn5gQCglpkI5UJvL8TbR5mtqF+tNBJo xcQAoKnRh486Yn73eiJKEPpXPB1DRyfh =87A/ -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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Need help!!!
#ZHAO LINA# wrote: But it's a bit trivial to modify those things if you just following those steps by steps. Using the latest version can save lots of works. Indeed. But I'm also a fan of solving one problem at a time. A broken force field file won't get fixed by trying to simultaneously accommodate a new organization and understand the intrinsics of Gromacs. By the way, thanks for the website, I once followed that too (nearly step by step also). Glad it was useful. When you say nearly, were there parts that didn't make sense/didn't work? Thanks with best regards, lina P.S actually you can upgrade your website also. ^_^ I realize that. But I do not have the time to do it, nor will I anytime in the near future. I've got a system that works, and if users are comfortable enough with the tutorial as is, then (as you say) it should be easy to convert over to the new system. For anyone new to the game, it may be useful to do the tutorial as is, learn Gromacs a bit more thoroughly, then undertake an adventure :) -Justin From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Thursday, September 02, 2010 9:12 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Need help!!! #ZHAO LINA# wrote: Make sure your gromacs is the latest version. If not, update and try again. The tutorial is specifically written for version 4.0.5, but will be compatible with any version 4.5. Since the re-organization of the force field directories, the information provided in the tutorial is not correct. I would recommend not upgrading until the OP has sorted out the problem and can then (maybe) work out the appropriate translation to the version 4.5.x scheme. -Justin *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of praba vathy [sumipraba2...@gmail.com] *Sent:* Thursday, September 02, 2010 9:06 PM *To:* gmx-users@gromacs.org *Subject:* [gmx-users] Need help!!! Hi, I am using simulation for a membrane protein. So i have downloaded the dppc.pdb along with it's topology files. I have used the following steps for the simulation (Based on the link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/01_pdb2gmx.html). We have used the commands and steps as described in the above link. But we have got a fatal error (Atom type C not found) while running this command, grompp -f mini.mdp -c dppc128.gro -p topol_dppc.top -o em.tp http://em.tp I cant sort out this problem. Please anybody help me to sort out this problem. Awaiting for your valuable replies. Praba -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Help regading Gromacs
For building membrane/protein systems I recommend charmm-gui.org The server automatically builds the coordinates, which you should be able to use with any modeling program; CHARMM equilibration scripts are generated as well Krzysztof On 9/2/10 6:20 AM, Justin A. Lemkul wrote: Please keep all Gromacs-related correspondence on the gmx-users list. I am not a private help service. I am CC'ing the message there; please continue any discussion via the forum. Creating a lipid bilayer is not a particularly easy task. You can generate a leaflet by replicating the coordinates of one lipid molecule in the x-y plane using genbox, then create the facing leaflet by rotating the existing leaflet using editconf. Concatenate the files and you have yourself a bilayer (which will need extensive equilibration, of course). Adding water is trivial with genbox. -Justin praba vathy wrote: Dear Sir, I want to create a lipid bilayer in which protein is inserted and on the top of insertion i need to put the water molecules and then at the bottom as well. I don't understand that how to place the molecules using Gromacs. Please give suggestions. Regards, Prabha. K -- Krzysztof Kuczera Professor Departments of Chemistry and Molecular Biosciences The University of Kansas 2010 Malott Hall Lawrence, KS 66045 Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu http://oolung.chem.ku.edu/~kuczera/home.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] intermolecular distance restrains
Dear Gromacs Users, I am presently using gromacs4.5 beta(since I want implicit solvent). I wish to apply intermolecular distance restraints. To my surprise there is no merge option in pdb2gmx (although pdb2gnx -h, says it has). So is there a new alternative to create intermolecular distance restrains. Best, nahren -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] intermolecular distance restrains
nahren manuel wrote: Dear Gromacs Users, I am presently using gromacs4.5 beta(since I want implicit solvent). I No need to use a beta version, the official 4.5 has been released. wish to apply intermolecular distance restraints. To my surprise there is no merge option in pdb2gmx (although pdb2gnx -h, says it has). So is there a new alternative to create intermolecular distance restrains. Use pdb2gmx -chainsep. -Justin Best, nahren -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Restart Replica Exchange
Hi, I was wondering if anyone knows whether it is possible to restart a replica exchange simulation if it stops during the run. I tried it once before and got the error that all the replicas should be at the same time step for replica exchange. When I checked the time step of different replicas, there was a few 10s of picoseconds difference b/w them. Is there a way to circumvent this problem and restart replica exchange? Thanks, Nimesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Force Field = Residues PHE, TRP, TYR, HIS ?
HI Residues PHE, TRP, TYR, and HIS are carrying Rings, or say pi bonds. How does the Gromacs deal with polarity for all this four residues? Is a single charge assigned for each atom on the center of atoms of the four residues ? Is pi bond given for the four residues in the force field? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Force Field = Residues PHE, TRP, TYR, HIS ?
Hi Chih-Ying Lin, There's no such thing as a pi bond in a classical force field, bonds are merely connections with a certain distance based potential. Gromacs doesn't deal with polarity, the distribution of charges, etc. is part of the force field. Better check the papers relating to the force field you're using. On the other hand, you might already be able to find the answers to your questions in the residue database for the force field you're using... Cheers, Tsjerk On Thu, Sep 2, 2010 at 6:41 PM, Chih-Ying Lin chihying2...@gmail.com wrote: HI Residues PHE, TRP, TYR, and HIS are carrying Rings, or say pi bonds. How does the Gromacs deal with polarity for all this four residues? Is a single charge assigned for each atom on the center of atoms of the four residues ? Is pi bond given for the four residues in the force field? Thank you Lin -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology / University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problems to generate the Hessian Matrix
2010/9/2 Luis Paulo luis...@gmail.com Dear all I need to calculate the normal modes of a protein. I am trying to generate the hessian matrix with mdrun. But it did not generate the hessian matrix (nm.mtx). Thanks for some help Luis Scott -- Prof. Dr. Luis Paulo Scott CMCC- Centro de Matemática, Computação e Cognição Universidade Federal do ABC Grupo de Pesquisa em Biologia Computacional -- Prof. Dr. Luis Paulo Scott CMCC- Centro de Matemática, Computação e Cognição Universidade Federal do ABC Grupo de Pesquisa em Biologia Computacional -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] intermolecular distance restrains
Dear Gromacs Users, The problem actually is mine is a hexamer, ARBSCT (chains). I want RST to be merged into a single molecular topology. I am either able to merge RS or ST or RT but not the trimer as such. I am able to do with -merge in the previous (ver 4.0.7 of ) pdb2gmx. Best, nahren --- On Thu, 9/2/10, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] intermolecular distance restrains To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Thursday, September 2, 2010, 8:09 PM nahren manuel wrote: Dear Gromacs Users, I am presently using gromacs4.5 beta(since I want implicit solvent). I No need to use a beta version, the official 4.5 has been released. wish to apply intermolecular distance restraints. To my surprise there is no merge option in pdb2gmx (although pdb2gnx -h, says it has). So is there a new alternative to create intermolecular distance restrains. Use pdb2gmx -chainsep. -Justin Best, nahren -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problems to generate the Hessian Matrix
Luis Paulo wrote: 2010/9/2 Luis Paulo luis...@gmail.com mailto:luis...@gmail.com Dear all I need to calculate the normal modes of a protein. I am trying to generate the hessian matrix with mdrun. But it did not generate the hessian matrix (nm.mtx). Thanks for some help What was in your .mdp file? -Justin Luis Scott -- Prof. Dr. Luis Paulo Scott CMCC- Centro de Matemática, Computação e Cognição Universidade Federal do ABC Grupo de Pesquisa em Biologia Computacional -- Prof. Dr. Luis Paulo Scott CMCC- Centro de Matemática, Computação e Cognição Universidade Federal do ABC Grupo de Pesquisa em Biologia Computacional -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] intermolecular distance restrains
nahren manuel wrote: Dear Gromacs Users, The problem actually is mine is a hexamer, ARBSCT (chains). I want RST to be merged into a single molecular topology. I am either able to merge RS or ST or RT but not the trimer as such. How is the .pdb set up? Does it have both chain ID's and TER delimiters? What was your pdb2gmx command line? -Justin I am able to do with -merge in the previous (ver 4.0.7 of ) pdb2gmx. Best, nahren --- On *Thu, 9/2/10, Justin A. Lemkul /jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] intermolecular distance restrains To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Thursday, September 2, 2010, 8:09 PM nahren manuel wrote: Dear Gromacs Users, I am presently using gromacs4.5 beta(since I want implicit solvent). I No need to use a beta version, the official 4.5 has been released. wish to apply intermolecular distance restraints. To my surprise there is no merge option in pdb2gmx (although pdb2gnx -h, says it has). So is there a new alternative to create intermolecular distance restrains. Use pdb2gmx -chainsep. -Justin Best, nahren -- 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 /mc/compose?to=gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org /mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Restart Replica Exchange
- Original Message - From: Nimesh Jain nimeshjain2...@u.northwestern.edu Date: Friday, September 3, 2010 1:13 Subject: [gmx-users] Restart Replica Exchange To: Discussion list for GROMACS users gmx-users@gromacs.org Hi, I was wondering if anyone knows whether it is possible to restart a replica exchange simulation if it stops during the run. I tried it once before and got the error that all the replicas should be at the same time step for replica exchange. When I checked the time step of different replicas, there was a few 10s of picoseconds difference b/w them. Is there a way to circumvent this problem and restart replica exchange? This issue will normally only arise if your run finished abnormally. I seem to recall discussion of it somewhere. Perhaps you need to restart in a different manner (hint: telling us your command lines would have been useful), e.g. using the checkpoint files properly. Alternatively, since the differences cannot span a replica exchange, you could try running the lagging simulations in serial until they're all in sync. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Bioinformatics Symposium at C-DAC, Pune
The Bioinformatics Group at C-DAC, Pune is going to organize a Symposium on Accelerating Biology from December 14-16 2010 at VITS, Pune. You can register for the same at: http://pune.cdac.in/html/events/bioinfo/accelerating_biology/index.aspx Regards, -- Anirban Ghosh C-DAC, Pune, India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
