Re: [gmx-users] GROMACS 4.6 release is ready!
How nice it is. Cheers. Albert On 01/21/2013 09:09 AM, Mark Abraham wrote: Hi GROMACS users, The day is finally here - GROMACS 4.6 is out! As you've probably heard by now, there are lots of wonderful new performance features, including * a native GPU implementation layer - thanks to some heroic work from Szilard Pall and Berk Hess, with special thanks to Mark Berger Duncan Poole from NVIDIA for their excellent advice and support * new implementation of Verlet kernels with guaranteed buffered interactions, with very good energy conservation * brand new classical nonbonded interaction kernels, supporting any of SSE2, SSE4.1, AMD's 128-bit AVX with FMA support, or Intel's 256-bit AVX SIMD acceleration, for 30-50% faster performance * use of OpenMP for better intra-node scaling * much improved automatic load balancing, including between direct-space and PME nodes * improvements to integration algorithms, including lots of new free energy options You can find the code, release notes, installation instructions and test suite at the links below. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x http://www.gromacs.org/Documentation/Installation_Instructions http://gromacs.googlecode.com/files/regressiontests-4.6.tar.gz If you have downloaded a 4.6 tarball already, we encourage you to get the latest one - a last-minute bug fix forced us to change plans. PDF installation instructions, and an updated manual release will follow in the coming week. A 4.5.6 bug-fix release has been prepared, and all its fixes are present in 4.6. We're still preparing its release notes, and will announce the release shortly. For those of you using our git repository, please be advised that that last-minute bug fix required us to move the tag for the 4.6 release. Your repo will not change that for you automatically. Happy simulating! The GROMACS development team -- 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] question about fftw3 in gromacs 4.6 installation
Hello: I am compiling the latest gromacs 4.6 with command: cmake .. -DGMX_MPI=ON -DCMAKE_CXX_COMPILER=/soft/openmpi-1.4.3/bin/mpiCC -DCMAKE_C_COMPILER=//soft/openmpi-1.4.3/bin/mpicc -DCMAKE_INSTALL_PREFIX=/soft/gromacs4.6 -DGMX_GPU=OFF -DBUILD_SHARED_LIBS=OFF -DFFTW_INCLUDE_DIR=/soft/fftw-3.3.3/include and I get get the following messages. It seems that it doesn't take my own compiled FFTW but it used the system FFTW: -- -- found fftw3f, version 3.1.2 -- Looking for fftwf_plan_r2r_1d in /usr/lib64/libfftw3f.so -- Looking for fftwf_plan_r2r_1d in /usr/lib64/libfftw3f.so - found -- Looking for fftwf_have_simd_avx in /usr/lib64/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib64/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib64/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib64/libfftw3f.so - found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Looking for cheev_ -- Looking for cheev_ - found -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: FFTW_INCLUDE_DIR -- What's more, I compiled fftw3 with options: ./configure --enable-sse --enable-float --with-pic --prefix=/soft/fftw-3.3.3 --enable-single --enable-static --enable-mpi And I don't find libfftw3f.so in my installation directory: ls /soft/fftw-3.3.3/lib libfftw3f.a libfftw3f.la libfftw3f_mpi.a libfftw3f_mpi.la pkgconfig thank you very much best Albert -- 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] gromacs 4.6 GB/SA problem and poor performance
Im trying to run an md or em using an implicit solvation method using gromacs 4.6 but I always get the incorrect result. ICC version : icc 11.0 fftw version : 3.2.2 benchmark system is gromacs-gpubench gromacs-gpubench-dhfr.tar/CPU/dhfr-impl-inf.bench Angle,Proper Dih,Imp Dih,Nonpolar sol,LJ-14,Coulomb-14 energy are correct. but GB polarization energy is too low, LJ(SR),Coulomb(SR) energy are always zero. It seems that there is a bug in the program. Using gromacs 4.5. It works fine. gromacs 4.5.3 : 9.4ns/day gromacs 4.6 :2.4ns/day -- View this message in context: http://gromacs.5086.n6.nabble.com/gromacs-4-6-GB-SA-problem-and-poor-performance-tp5004728.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] conversion of Gromacs trajectories (rhombic dodecahedric), and topologies to Amber format
Dear gmx-users, I followed the suggestions by Justin and Daniel to convert the trajectories, but still Amber does not recognize the correct format and complains about the fact that it does not find the correct box dimensions. It seems that the two tools are quite incompatible, especially when the trajectory is not in the classic cubic format. This is just for records since it is a recurrent query in the gmx-user archive, still apparently with no solution. Many thanks in any case and best regards Anna -- __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Ponte don Melillo 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089 969603 E-mail: amarabo...@unisa.it Skype: annam1972 When a man with a gun meets a man with a pen, the man with the gun is a dead man (Roberto Benigni, about Roberto Saviano) -- 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] Run long-time MD process
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations On 01/21/2013 11:20 AM, Kieu Thu Nguyen wrote: Dear All, I intend to run a long-time MD process. Can i split it into many smaller processes without losing system properties ? Is that the following process will be followed from the results of the previous process ? Thank so much for any advice ! Regards, KT -- 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] conversion of Gromacs trajectories (rhombic dodecahedric), and topologies to Amber format
probably you can try catdcd On 01/21/2013 11:29 AM, Anna Marabotti wrote: Dear gmx-users, I followed the suggestions by Justin and Daniel to convert the trajectories, but still Amber does not recognize the correct format and complains about the fact that it does not find the correct box dimensions. It seems that the two tools are quite incompatible, especially when the trajectory is not in the classic cubic format. This is just for records since it is a recurrent query in the gmx-user archive, still apparently with no solution. Many thanks in any case and best regards Anna -- 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] Implicit sovent simulation with CHARMM FF
Hi, all I have trouble grompping my systems containing drug-like molecules. I am using Charmm parameter and the addion of atomtypes and pairtypes were all done. Under explicit condition everthing is alright and I also added the missing atomtypes in the gb.itp under the charmm.ff folder like this [ implicit_genborn_params ] ; Atom type sar st pi gbr hct ;2013.1.21. 7 new parameter based on approximate atom type CB 0.180 1 1.073 0.1875 0.72 ; CA SMMF 0.180 1 1.121 0.1775 0.96 ; S CR 0.200 1 0.880 0.1900.72 ; CT3 OR 0.152 1 1.080 0.1535 0.85 ; OH1 HCMM 0.1 1 1 0.1250.85 ; HA HOCC 0.1 1 1 0.1150.85 ; H HOR0.1 1 1 0.1150.85 ; H But I still got error when running grompp: Couldn't find topology match for atomtype CB Aborted I'v scanned the mail list and althouth this problem has been disccussed , it seems there is no direct answer for it. Anyone knows where to add extra parameter for these 7 new atomtypes? Sincerely, 2013-01-21 zxchen, Ph.D -- 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: Implicit sovent simulation with CHARMM FF
Sorry..I'v made a stupid mistake annotating some lines in the .itp file. I'v fixed it. 2013-01-21 supermanczx 发件人： supermanczx 发送时间： 2013-01-21 18:59:20 收件人： gmx-users 抄送： 主题： Implicit sovent simulation with CHARMM FF Hi, all I have trouble grompping my systems containing drug-like molecules. I am using Charmm parameter and the addion of atomtypes and pairtypes were all done. Under explicit condition everthing is alright and I also added the missing atomtypes in the gb.itp under the charmm.ff folder like this [ implicit_genborn_params ] ; Atom type sar st pi gbr hct ;2013.1.21. 7 new parameter based on approximate atom type CB 0.180 1 1.073 0.1875 0.72 ; CA SMMF 0.180 1 1.121 0.1775 0.96 ; S CR 0.200 1 0.880 0.1900.72 ; CT3 OR 0.152 1 1.080 0.1535 0.85 ; OH1 HCMM 0.1 1 1 0.1250.85 ; HA HOCC 0.1 1 1 0.1150.85 ; H HOR0.1 1 1 0.1150.85 ; H But I still got error when running grompp: Couldn't find topology match for atomtype CB Aborted I'v scanned the mail list and althouth this problem has been disccussed , it seems there is no direct answer for it. Anyone knows where to add extra parameter for these 7 new atomtypes? Sincerely, 2013-01-21 zxchen, Ph.D -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GROMACS 4.6 release is ready!
That is really great..Thanks for all the work on this! Cheers, Davide On 21/01/13 9:09 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi GROMACS users, The day is finally here - GROMACS 4.6 is out! As you've probably heard by now, there are lots of wonderful new performance features, including * a native GPU implementation layer - thanks to some heroic work from Szilard Pall and Berk Hess, with special thanks to Mark Berger Duncan Poole from NVIDIA for their excellent advice and support * new implementation of Verlet kernels with guaranteed buffered interactions, with very good energy conservation * brand new classical nonbonded interaction kernels, supporting any of SSE2, SSE4.1, AMD's 128-bit AVX with FMA support, or Intel's 256-bit AVX SIMD acceleration, for 30-50% faster performance * use of OpenMP for better intra-node scaling * much improved automatic load balancing, including between direct-space and PME nodes * improvements to integration algorithms, including lots of new free energy options You can find the code, release notes, installation instructions and test suite at the links below. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x http://www.gromacs.org/Documentation/Installation_Instructions http://gromacs.googlecode.com/files/regressiontests-4.6.tar.gz If you have downloaded a 4.6 tarball already, we encourage you to get the latest one - a last-minute bug fix forced us to change plans. PDF installation instructions, and an updated manual release will follow in the coming week. A 4.5.6 bug-fix release has been prepared, and all its fixes are present in 4.6. We're still preparing its release notes, and will announce the release shortly. For those of you using our git repository, please be advised that that last-minute bug fix required us to move the tag for the 4.6 release. Your repo will not change that for you automatically. Happy simulating! The GROMACS development team -- 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] gromacs 4.6 GB/SA problem and poor performance
On 2013-01-21 09:55, Changwon Yang wrote: Im trying to run an md or em using an implicit solvation method using gromacs 4.6 but I always get the incorrect result. ICC version : icc 11.0 fftw version : 3.2.2 benchmark system is gromacs-gpubench gromacs-gpubench-dhfr.tar/CPU/dhfr-impl-inf.bench Angle,Proper Dih,Imp Dih,Nonpolar sol,LJ-14,Coulomb-14 energy are correct. but GB polarization energy is too low, LJ(SR),Coulomb(SR) energy are always zero. It seems that there is a bug in the program. Using gromacs 4.5. It works fine. gromacs 4.5.3 : 9.4ns/day gromacs 4.6 :2.4ns/day Can you please file a redmine issue with sample input files? http://redmine.gromacs.org Thanks! -- View this message in context: http://gromacs.5086.n6.nabble.com/gromacs-4-6-GB-SA-problem-and-poor-performance-tp5004728.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] g_bar Fatal error: There is no proper lambda legend
Dear GROMACS developers, I was using gmx-4.6.b3 to run a simple FEP simulation for calculating the solvation free energy of ions in water. The simulations run ok. However, when I tried to use g_bar with the dhdl.xvg files, I received the following error: There is no proper lambda legend in file 'lambda_0.0/md.xvg', can not deduce lambda. File md.xvg is attached. Thank you! Elena Lilkova -- 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] question about fftw3 in gromacs 4.6 installation
On 1/21/13 3:44 AM, Albert wrote: Hello: I am compiling the latest gromacs 4.6 with command: cmake .. -DGMX_MPI=ON -DCMAKE_CXX_COMPILER=/soft/openmpi-1.4.3/bin/mpiCC -DCMAKE_C_COMPILER=//soft/openmpi-1.4.3/bin/mpicc -DCMAKE_INSTALL_PREFIX=/soft/gromacs4.6 -DGMX_GPU=OFF -DBUILD_SHARED_LIBS=OFF -DFFTW_INCLUDE_DIR=/soft/fftw-3.3.3/include and I get get the following messages. It seems that it doesn't take my own compiled FFTW but it used the system FFTW: -- -- found fftw3f, version 3.1.2 -- Looking for fftwf_plan_r2r_1d in /usr/lib64/libfftw3f.so -- Looking for fftwf_plan_r2r_1d in /usr/lib64/libfftw3f.so - found -- Looking for fftwf_have_simd_avx in /usr/lib64/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib64/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib64/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib64/libfftw3f.so - found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Looking for cheev_ -- Looking for cheev_ - found -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: FFTW_INCLUDE_DIR -- What's more, I compiled fftw3 with options: ./configure --enable-sse --enable-float --with-pic --prefix=/soft/fftw-3.3.3 --enable-single --enable-static --enable-mpi And I don't find libfftw3f.so in my installation directory: That's because you used --enable-static. A .so file is a shared object. ls /soft/fftw-3.3.3/lib libfftw3f.a libfftw3f.la libfftw3f_mpi.a libfftw3f_mpi.la pkgconfig Your cmake command needs to use -DFFTWF_INCLUDE_DIR and -DFFTWF_LIBRARY to indicate the single-precision libraries (note that -DFFTW_INCLUDE_DIR and -DFFTWF_INCLUDE_DIR specify different things) or simply use -DCMAKE_PREFIX_PATH=/soft/fftw-3.3.3/ for convenience. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] calculate area per lipid and bilayer thickness versus time
On 1/21/13 5:12 AM, Kieu Thu Nguyen wrote: Dear All, I want to know that my lipid bilayer is equilibrated or not yet. So i want to calculate the change of area per lipid and the bilayer thickness versus time. Which tool or method should i use ? Extract box vectors over time from the .edr file, then use a script of your own creation to multiply them and divide by the number of lipids per leaflet. Of course, that goes out the window if there is a protein present. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_bar Fatal error: There is no proper lambda legend
On 1/21/13 7:31 AM, Elena Lilkova wrote: Dear GROMACS developers, I was using gmx-4.6.b3 to run a simple FEP simulation for calculating the solvation free energy of ions in water. The simulations run ok. However, when I tried to use g_bar with the dhdl.xvg files, I received the following error: There is no proper lambda legend in file 'lambda_0.0/md.xvg', can not deduce lambda. Please upgrade to the released version 4.6 and try again. There were several fixes to the free energy code. If the problem persists, please post again. File md.xvg is attached. Attachments are not allowed, FYI. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] could not understand force.xvg file
On 1/21/13 8:27 AM, biki wrote: Hi , I am doing a simulation of 32 spce water molecules using Gromacs-4.5.5 version. I need to calculate the force on each hydrogen atom of each water molecule due to all other atoms on rest 31 water molecules. I have generated the force.xvg file and I know that it will print the x,y and z component of force on each hydrogen as a function of time. But when I opened it in vi editor, it was not legible at all. I have attached a snapshot of force.xvg file here. Can any one please explain how this force.xvg file is arranged? Is there any way to write these forces in a format mentioned below by using gromacs utility time step x-component of force on Hydrogen1 y-component of force on Hydrogen1 z-component of force on Hydrogen1 x-component of force on Hydrogen2 y-component of force on Hydrogen2 z-component of force on Hydrogen2 . . . so on That's what you have, but since it's a time-dependent quantity, these values are printed for every frame in the trajectory. Note the legends present. You have 96 atoms, each with the (x,y,z) components of the force printed for each frame. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] question about fftw3 in gromacs 4.6 installation
On 01/21/2013 01:31 PM, Justin Lemkul wrote: Your cmake command needs to use -DFFTWF_INCLUDE_DIR and -DFFTWF_LIBRARY to indicate the single-precision libraries (note that -DFFTW_INCLUDE_DIR and -DFFTWF_INCLUDE_DIR specify different things) or simply use -DCMAKE_PREFIX_PATH=/soft/fftw-3.3.3/ for convenience. -Justin Hello Justin: thank you very much for kind comments. It works now. best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gromacs 4.6 GB/SA problem and poor performance
On Mon, Jan 21, 2013 at 3:55 AM, Changwon Yang sht_yc...@hotmail.comwrote: Im trying to run an md or em using an implicit solvation method using gromacs 4.6 but I always get the incorrect result. ICC version : icc 11.0 fftw version : 3.2.2 benchmark system is gromacs-gpubench gromacs-gpubench-dhfr.tar/CPU/dhfr-impl-inf.bench Angle,Proper Dih,Imp Dih,Nonpolar sol,LJ-14,Coulomb-14 energy are correct. but GB polarization energy is too low, LJ(SR),Coulomb(SR) energy are always zero. It seems that there is a bug in the program. Using gromacs 4.5. It works fine. gromacs 4.5.3 : 9.4ns/day gromacs 4.6 :2.4ns/day Please provide the output of mdrun -version. Also ICC 11.0 is quite old. Please test whether the same issue is present with a more recent ICC or GCC compiler. Roland -- View this message in context: http://gromacs.5086.n6.nabble.com/gromacs-4-6-GB-SA-problem-and-poor-performance-tp5004728.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] how can I make statics for Z-axis?
hello: I would like to make statics for an atom along Z-axis. I am just wondering how can I to do this in Gromacs? thank you very much best Albert -- 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] calculate area per lipid and bilayer thickness versus time
Thank Justin ! That is APL. How about bilayer thickness ? I made density.xvg file of headgroup from using g_density. On Mon, Jan 21, 2013 at 7:31 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/21/13 5:12 AM, Kieu Thu Nguyen wrote: Dear All, I want to know that my lipid bilayer is equilibrated or not yet. So i want to calculate the change of area per lipid and the bilayer thickness versus time. Which tool or method should i use ? Extract box vectors over time from the .edr file, then use a script of your own creation to multiply them and divide by the number of lipids per leaflet. Of course, that goes out the window if there is a protein present. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Run long-time MD process
Thank Felipe ! :-) On Mon, Jan 21, 2013 at 5:30 PM, Felipe Pineda, PhD luis.pinedadecas...@lnu.se wrote: http://www.gromacs.org/**Documentation/How-tos/**Extending_Simulationshttp://www.gromacs.org/Documentation/How-tos/Extending_Simulations On 01/21/2013 11:20 AM, Kieu Thu Nguyen wrote: Dear All, I intend to run a long-time MD process. Can i split it into many smaller processes without losing system properties ? Is that the following process will be followed from the results of the previous process ? Thank so much for any advice ! Regards, KT -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] inquiring for solving trjconv problems
On 1/21/13 11:00 AM, Mehdi Bagherpour wrote: hello justin I used *make_ndx -f md.tpr: 0 System : 35194 atoms 1 DNA : 1012 atoms 2 MG : 4 atoms 3 CL :29 atoms 4 K :51 atoms 5 Water : 34098 atoms 6 SOL : 34098 atoms 7 non-Water : 1096 atoms 8 Other : 4 atoms 9 MG : 4 atoms 10 CL :29 atoms 11 K :51 atoms 12 Ion :80 atoms 13 MG : 4 atoms 14 CL :29 atoms 15 K :51 atoms 16 Water_and_ions : 34178 atoms nr : group ! 'name' nr name 'splitch' nrEnter: list groups 'a': atom 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr'splitat' nr'h': help 'r': residue 'res' nr 'chain' char name: group'case': case sensitive 'q': save and quit 'ri': residue index 1 Copied index group 1 'DNA' 17 DNA : 1012 atoms* then I used from bellow command: *trjconv -s md.tpr -f md.xtc -n index.ndx -o md_1.xtc -center* and then: *trjconv -s md.tpr -f md_1.xtc -n index.ndx -o md.pdb -pbc mol -ur compact* but problem is not fixed. Because you're not doing anything productive. You're just copying an existing group that has already been demonstrated to be ineffective. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] calculate area per lipid and bilayer thickness versus time
On 1/21/13 10:17 AM, Kieu Thu Nguyen wrote: Thank Justin ! That is APL. How about bilayer thickness ? I made density.xvg file of headgroup from using g_density. g_dist with index groups specifying however you want to define the boundaries for the membrane, or (shameless plug) a lateral projection of thickness (from which an average can easily be derived: http://bevanlab.biochem.vt.edu/GridMAT-MD/. -Justin On Mon, Jan 21, 2013 at 7:31 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/21/13 5:12 AM, Kieu Thu Nguyen wrote: Dear All, I want to know that my lipid bilayer is equilibrated or not yet. So i want to calculate the change of area per lipid and the bilayer thickness versus time. Which tool or method should i use ? Extract box vectors over time from the .edr file, then use a script of your own creation to multiply them and divide by the number of lipids per leaflet. Of course, that goes out the window if there is a protein present. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problem with gromacs-4.6 compilation on Debian
Hi, Not sure why, but it looks like libcudart.so is linked against a glibc that not compatible with what you have (perhaps much newer)? Alternatively you could try adding --add-needed to the linker flags, but I doubt it will help. Cheers, -- Szilárd On Mon, Jan 21, 2013 at 5:09 PM, James Starlight jmsstarli...@gmail.comwrote: Dear Gromacs Users! I've successfully installed Gromacs-4.6 on my Debian mint system but on another ( classic Debian) I've obtained error during make step (in both cases I'm using 64 bit debian): [ 55%] Building C object share/template/CMakeFiles/template.dir/template.c.o Linking CXX executable template /usr/local/cuda-5.0/lib64/libcudart.so: undefined reference to `std::__detail::_List_node_base::_M_unhook()@GLIBCXX_3.4.15' /usr/local/cuda-5.0/lib64/libcudart.so: undefined reference to `std::__detail::_List_node_base::_M_hook(std::__detail::_List_node_base*)@GLIBCXX_3.4.15' collect2: ld returned 1 exit status make[2]: *** [share/template/template] Error 1 make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 make: *** [all] Error 2 In both cases I've used gcc-4.4 for compilation with cuda-5. What's wrong? James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] Getting the virial for each individual atom.
Hello, For the research I'm working with, I need to get the virial for each individual atom in the system. I've been tracing all of the calls made in the methods related to virials(Version 4.5.5) and this is the call stack that I think has what I need. mdrun.c - do_md in md.c - do_force in sim_util.c - calcvir.c I have a few questions that I was wondering if anyone could answer. 1. In sim_util.c, there is a comment that says Total virial computed in global_stat, called from do_md. I cannot find where this is called in do_md. Was this changed at any point and the comment was still left in the code? 2. If I change the codes in calcvir.c to find the virials for each individual atom, say by piping the atom numbers and forces and everything needed into another program so it doesn't effect the way that gromacs runs and will still allow everything to do what it needs, will this be screwed up by/screw up the domain decomposition/the mpi stuff? Basically, I'm looking for advice on a method to output the individual virials for each atom for each frame, instead of just the final output of the average virial on the entire system. Thanks, Zach Marcin Wilkes University -- 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] Getting the virial for each individual atom.
Hi, The virial has no meaning per atom. And you can't get the virial per atom out of Gromacs, it is never calculated in that way (see the manual for details). A special local pressure version of Gromacs exists, but even there you won't get a virial per atom. Cheers, Berk Date: Mon, 21 Jan 2013 12:35:04 -0500 From: zachary.mar...@wilkes.edu To: gmx-users@gromacs.org Subject: [gmx-users] Getting the virial for each individual atom. Hello, For the research I'm working with, I need to get the virial for each individual atom in the system. I've been tracing all of the calls made in the methods related to virials(Version 4.5.5) and this is the call stack that I think has what I need. mdrun.c - do_md in md.c - do_force in sim_util.c - calcvir.c I have a few questions that I was wondering if anyone could answer. 1. In sim_util.c, there is a comment that says Total virial computed in global_stat, called from do_md. I cannot find where this is called in do_md. Was this changed at any point and the comment was still left in the code? 2. If I change the codes in calcvir.c to find the virials for each individual atom, say by piping the atom numbers and forces and everything needed into another program so it doesn't effect the way that gromacs runs and will still allow everything to do what it needs, will this be screwed up by/screw up the domain decomposition/the mpi stuff? Basically, I'm looking for advice on a method to output the individual virials for each atom for each frame, instead of just the final output of the average virial on the entire system. Thanks, Zach Marcin Wilkes University -- 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
Re: [gmx-users] Getting the virial for each individual atom.
Berk, Here is where I think I might be able to: In calcvir.c there is a method called calc_vir which takes, among other things, int nxf(no idea what this does), rvec x[], and revec f[]. It then does dvxx+= x[i][xx] *f[i][XX];. This is the same as the formula that I am trying to solve for (Vi*Pi + .5*SUM(Rij * Fij)). What I figured I could do is create another array to calculate the virials for, thus giving me an index position per atom, and then use that somehow. I also know that I can use R(ij) * F(ij), or the distance between atoms i and j times the Forces between atoms i and j. If anyone has any insight on getting these, that could also work. I know how to get the individual positions, but I don't know how I would go about the forces aspect of that. Thanks, Zach On Mon, Jan 21, 2013 at 12:44 PM, Berk Hess g...@hotmail.com wrote: Hi, The virial has no meaning per atom. And you can't get the virial per atom out of Gromacs, it is never calculated in that way (see the manual for details). A special local pressure version of Gromacs exists, but even there you won't get a virial per atom. Cheers, Berk Date: Mon, 21 Jan 2013 12:35:04 -0500 From: zachary.mar...@wilkes.edu To: gmx-users@gromacs.org Subject: [gmx-users] Getting the virial for each individual atom. Hello, For the research I'm working with, I need to get the virial for each individual atom in the system. I've been tracing all of the calls made in the methods related to virials(Version 4.5.5) and this is the call stack that I think has what I need. mdrun.c - do_md in md.c - do_force in sim_util.c - calcvir.c I have a few questions that I was wondering if anyone could answer. 1. In sim_util.c, there is a comment that says Total virial computed in global_stat, called from do_md. I cannot find where this is called in do_md. Was this changed at any point and the comment was still left in the code? 2. If I change the codes in calcvir.c to find the virials for each individual atom, say by piping the atom numbers and forces and everything needed into another program so it doesn't effect the way that gromacs runs and will still allow everything to do what it needs, will this be screwed up by/screw up the domain decomposition/the mpi stuff? Basically, I'm looking for advice on a method to output the individual virials for each atom for each frame, instead of just the final output of the average virial on the entire system. Thanks, Zach Marcin Wilkes University -- 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 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] Digedral Angle for aa?
How can we Plot the X1,X2 angle (degree) wise time point for single amino acids? Can g_angle or g_chi can do ?-- 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] Digedral Angle for aa?
On 1/21/13 1:08 PM, 라지브간디 wrote: How can we Plot the X1,X2 angle (degree) wise time point for single amino acids? Can g_angle or g_chi can do ? g_angle seems to be the most straightforward way. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Getting the virial for each individual atom.
On Mon, Jan 21, 2013 at 7:06 PM, Marcin, Zachary zachary.mar...@wilkes.eduwrote dvxx+= x[i][xx] *f[i][XX]; Compare the indexing above with: This is the same as the formula that I am trying to solve for (Vi*Pi + .5*SUM(Rij * Fij)). ... the ones you want to have. See the difference ? The existing code takes one atom at a time (i), what you want takes 2 atoms at a time (i j). You cannot calculate what you want from there, as the forces are already summed per atom; Fij are the pairwise forces calculated in the kernels corresponding to the different potentials. Cheers, Bogdan -- 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] clusterization in dihedral space
On 1/21/13 1:54 PM, francesco oteri wrote: Dear gromacs users, I am trying to run dihedral space clustering with g_dih, but I found that it gives me a lot of error like: Dihedral around 24,26 not found in topology. Using mult=3 Looking on the net, I found something alarming: g_dih is gromos specific! http://lists.gromacs.org/pipermail/gmx-users/2006-August/023230.html It is still true? Yes, and it is for this reason that g_dih has been removed from Gromacs. You can likely accomplish whatever you're trying to do with g_angle. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] clusterization in dihedral space
Thank you, but I don't see how performing cluster analysis with g_angle Francesco 2013/1/21 Justin Lemkul jalem...@vt.edu On 1/21/13 1:54 PM, francesco oteri wrote: Dear gromacs users, I am trying to run dihedral space clustering with g_dih, but I found that it gives me a lot of error like: Dihedral around 24,26 not found in topology. Using mult=3 Looking on the net, I found something alarming: g_dih is gromos specific! http://lists.gromacs.org/**pipermail/gmx-users/2006-**August/023230.htmlhttp://lists.gromacs.org/pipermail/gmx-users/2006-August/023230.html It is still true? Yes, and it is for this reason that g_dih has been removed from Gromacs. You can likely accomplish whatever you're trying to do with g_angle. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] clusterization in dihedral space
On 1/21/13 2:06 PM, francesco oteri wrote: Thank you, but I don't see how performing cluster analysis with g_angle You may have to do some post-processing yourself, but g_angle can certainly measure dihedrals and produce distributions. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Getting the virial for each individual atom.
Zach, Do you have periodic system with charges? For PBC, you might try one of the forms in J. Chem. Phys. 131 154107 (2009). Electrostatics are more work... For Ewald sum and PPPM contribution, you could check refs in lammps.sandia.gov/doc/PDF/kspace.pdf We have an upcoming paper that explains in more detail how to do this with PPPM and gives an example with heat flux. Maybe something similar could be done in GROMACS with PME. best, Tim On Mon, Jan 21, 2013 at 1:06 PM, Marcin, Zachary zachary.mar...@wilkes.eduwrote: Berk, Here is where I think I might be able to: In calcvir.c there is a method called calc_vir which takes, among other things, int nxf(no idea what this does), rvec x[], and revec f[]. It then does dvxx+= x[i][xx] *f[i][XX];. This is the same as the formula that I am trying to solve for (Vi*Pi + .5*SUM(Rij * Fij)). What I figured I could do is create another array to calculate the virials for, thus giving me an index position per atom, and then use that somehow. I also know that I can use R(ij) * F(ij), or the distance between atoms i and j times the Forces between atoms i and j. If anyone has any insight on getting these, that could also work. I know how to get the individual positions, but I don't know how I would go about the forces aspect of that. Thanks, Zach On Mon, Jan 21, 2013 at 12:44 PM, Berk Hess g...@hotmail.com wrote: Hi, The virial has no meaning per atom. And you can't get the virial per atom out of Gromacs, it is never calculated in that way (see the manual for details). A special local pressure version of Gromacs exists, but even there you won't get a virial per atom. Cheers, Berk Date: Mon, 21 Jan 2013 12:35:04 -0500 From: zachary.mar...@wilkes.edu To: gmx-users@gromacs.org Subject: [gmx-users] Getting the virial for each individual atom. Hello, For the research I'm working with, I need to get the virial for each individual atom in the system. I've been tracing all of the calls made in the methods related to virials(Version 4.5.5) and this is the call stack that I think has what I need. mdrun.c - do_md in md.c - do_force in sim_util.c - calcvir.c I have a few questions that I was wondering if anyone could answer. 1. In sim_util.c, there is a comment that says Total virial computed in global_stat, called from do_md. I cannot find where this is called in do_md. Was this changed at any point and the comment was still left in the code? 2. If I change the codes in calcvir.c to find the virials for each individual atom, say by piping the atom numbers and forces and everything needed into another program so it doesn't effect the way that gromacs runs and will still allow everything to do what it needs, will this be screwed up by/screw up the domain decomposition/the mpi stuff? Basically, I'm looking for advice on a method to output the individual virials for each atom for each frame, instead of just the final output of the average virial on the entire system. Thanks, Zach Marcin Wilkes University -- 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 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] Parallelization scheme and terminology help
I have been lost in the sea of terminology for installing gromacs with multi-processors. The plan is to upgrade from 4.5.5 to the 4.6 and i want the optimal install for my system. There is a a nice explanaion at http://www.gromacs.org/Documentation/Acceleration_and_parallelization but the number of different options and terminology has confused me. I currently have one computer with 2 processor sockets each with 4 cores each with 2 threads. A mouthful which in the end allows for 16 processes at once(2*4*2). The way i read the documentation is that MPI is needed for the talk between the 2 physical processors, OpenMP does the talk between the 4 cores in each processor and thread-MPI does the treading? or does thread-MPI do everything? What would be the Parallelization scheme is required? -- 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] Parallelization scheme and terminology help
On Mon, Jan 21, 2013 at 11:50 PM, Brad Van Oosten bv0...@brocku.ca wrote: I have been lost in the sea of terminology for installing gromacs with multi-processors. The plan is to upgrade from 4.5.5 to the 4.6 and i want the optimal install for my system. There is a a nice explanaion at http://www.gromacs.org/**Documentation/Acceleration_**and_parallelizationhttp://www.gromacs.org/Documentation/Acceleration_and_parallelizationbut the number of different options and terminology has confused me. That's life, unfortunately. Nomenclature is poorly standardized and gets re-used by different vendors to mean different things, or in different contexts. I currently have one computer with 2 processor sockets each with 4 cores each with 2 threads. A mouthful which in the end allows for 16 processes at once(2*4*2). Your sockets don't require a network to talk to each other, so thread-mpi suffices. Probably your threads are hyper-threads, which may or may not be useful for GROMACS. But you will need to read actual documentation and look up chip set descriptions to really know what you have. The way i read the documentation is that MPI is needed for the talk between the 2 physical processors, OpenMP does the talk between the 4 cores in each processor and thread-MPI does the treading? or does thread-MPI do everything? What would be the Parallelization scheme is required? Probably, use ThreadMPI and forget about everything else :-) This question cannot be answered in the abstract (you'd need to know full hardware characteristics and simulation system characteristics). It is best assessed by trying a few options and comparing the throughput you observe on the systems you care about. 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/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] inquiring for solving trjconv problems
Hello Justin My problem is fixed I am very grateful for your help. I used from bellow commands: * * *1- make_ndx -f md.tpr * *r 1-16 -DNA have 32 residue 2- trjconv -s md.tpr -f wi_md.xtc -n index.ndx -o md.pdb -center -pbc mol * *2-1- for centering --- residue 1-16 --- new group * *2-2- for pbc DNA group 1* You have been a big help to me. So Thanks -- 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: gromacs 4.6 GB/SA problem and poor performance
Input files: conf.gro and mdp files http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GROMACS-OpenMM cpu-imp-RF-inf.mdp constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 0 nstlist = 0 ns_type = grid rlist = 0 coulombtype = cut-off vdwtype = cut-off rcoulomb= 0 rvdw= 0 pbc = no epsilon_rf = 0 rgbradii= 0 comm_mode = angular implicit_solvent= GBSA gb_algorithm= OBC gb_epsilon_solvent = 78.3 sa_surface_tension = 2.25936 nstxout = 0 nstfout = 0 nstvout = 0 nstxtcout = 50 nstlog = 0 nstcalcenergy = -1 nstenergy = 50 tcoupl = berendsen tc-grps = system tau-t = 0.1 ref-t = 300 gromacs 4.6 (icc 11.0, centos 5.8, fftw 3.2.2) Statistics over 101 steps [ 0. through 0.2000 ps ], 10 data sets All statistics are over 11 points Energy Average Err.Est. RMSD Tot-Drift --- Angle 4189.86 --1094.252527.08 (kJ/mol) Proper Dih. 6600.66 --234.905471.156 (kJ/mol) Improper Dih. 121.598 --32.7574 64.572 (kJ/mol) GB Polarization-32708.8 --1979.66 -6416.79 (kJ/mol) Nonpolar Sol. 158.323 --13.0032 42.232 (kJ/mol) LJ-14 2346.66 --180.767289.567 (kJ/mol) Coulomb-14 26555.4 --1091.98 -3000.88 (kJ/mol) LJ (SR) 0 -- 0 0 (kJ/mol) Coulomb (SR) 0 -- 0 0 (kJ/mol) Potential 7263.71 --1835.42 -6023.06 (kJ/mol) gromacs 4.5.3 Statistics over 101 steps [ 0. through 0.2000 ps ], 10 data sets All statistics are over 11 points Energy Average Err.Est. RMSD Tot-Drift --- Angle 1840.12 --178.343561.256 (kJ/mol) Proper Dih.6207 --101.135210.593 (kJ/mol) Improper Dih. 68.4513 --11.621429.5806 (kJ/mol) GB Polarization-13534.1 --34.366695.8711 (kJ/mol) Nonpolar Sol. 143.048 --1.558685.13589 (kJ/mol) LJ-14 2380.44 --26.956324.6177 (kJ/mol) Coulomb-14 29155.5 --64.9054 -176.267 (kJ/mol) LJ (SR)-5274.28 --214.048650.865 (kJ/mol) Coulomb (SR) -38297.8 --143.656 -398.004 (kJ/mol) Potential -17311.7 --451.5811003.65 (kJ/mol) In gromacs 4.5.3 GB/SA problem Starting from fully linear peptide and using inf cut-off, I always get the segmentation fault error. Using finite cut-off, It works fine. -- View this message in context: http://gromacs.5086.n6.nabble.com/gromacs-4-6-GB-SA-problem-and-poor-performance-tp5004729p5004778.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] calculate area per lipid and bilayer thickness versus time
Thank Justin ! And i used GridMAT-MD as you advised. I got result The average bilayer thickness will be printed to 50x50_average_pbc.dat. But that result is only equal to a half of experiment result. I think bilayer thickness is equal to the sum of top leaflet thickness and bottom leaflet thickness. So should i double The average bilayer thickness... mentioned above ? And i do not get average area per lipd, just The average area per lipid in the top leaflet is 64.2329395973154 sq. Angstroms. The average area per lipid in the bottom leaflet is 63.3821721854305 sq. Angstroms. Thanks in advance ! KT On Mon, Jan 21, 2013 at 11:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/21/13 10:17 AM, Kieu Thu Nguyen wrote: Thank Justin ! That is APL. How about bilayer thickness ? I made density.xvg file of headgroup from using g_density. g_dist with index groups specifying however you want to define the boundaries for the membrane, or (shameless plug) a lateral projection of thickness (from which an average can easily be derived: http://bevanlab.biochem.vt.**edu/GridMAT-MD/http://bevanlab.biochem.vt.edu/GridMAT-MD/ . -Justin On Mon, Jan 21, 2013 at 7:31 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/21/13 5:12 AM, Kieu Thu Nguyen wrote: Dear All, I want to know that my lipid bilayer is equilibrated or not yet. So i want to calculate the change of area per lipid and the bilayer thickness versus time. Which tool or method should i use ? Extract box vectors over time from the .edr file, then use a script of your own creation to multiply them and divide by the number of lipids per leaflet. Of course, that goes out the window if there is a protein present. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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
