Re: [gmx-users] (no subject)
Sir, Can anyone suggest how I can use ethanol force field to solvate and run MD for my molecule. Please help. On Thu 31 Jan, 2019, 10:48 AM Satya Ranjan Sahoo Sir, > I am a beginner to GROMACS. I was unable to understand how to create all > the ions.mdp , md.mdp , mout.mdp , minim.mdp , newbox.mdp , npt.mdp , > nvt.mdp , porse.itp , topol.top input files for molecular simulation of my > molecule. Please teach me how can I generate or create all the above > mentioned input files for my molecule. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] (no subject)
Sir, I am a beginner to GROMACS. I was unable to understand how to create all the ions.mdp , md.mdp , mout.mdp , minim.mdp , newbox.mdp , npt.mdp , nvt.mdp , porse.itp , topol.top input files for molecular simulation of my molecule. Please teach me how can I generate or create all the above mentioned input files for my molecule. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Version problem
Dear Dr. Carsten Kutzner, I am unable to find the gmx5/bin/GMXRC in my machine, used 'locate' and 'find' to search the location. However I have source the following: source /usr/share/gromacs/shell-specific/GMXRC.bashrc Without this also mdrun is running. I am definitely missing something. Kindly help. With best regards, Satya On 06 Nov 2014, at 07:15, sa...@physics.iisc.ernet.in wrote: Dear all, I am new to GROMACS, just finish installation of v5.0.2, started reading online manual, as instructed executed the command: mdrun -version and the printout pasted below. It is printing GROMACS version 4.6.5, however I have installed version 5.0.2. What is the problem? Find the directory to where you have installed your GROMACS 5.0 executables and then do source /path/to/gmx5/bin/GMXRC which mdrun should now give you the 5.0 mdrun Carsten Regards, Satyabrata Das == Program: mdrun Gromacs version:VERSION 4.6.5 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled GPU support:disabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: SSE4.1 FFT library:fftw-3.3.3-sse2-avx Large file support: enabled RDTSCP usage: enabled Built on: Sun Dec 15 04:01:11 UTC 2013 Built by: buildd@panlong [CMAKE] Build OS/arch: Linux 3.2.0-37-generic x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Xeon(R) CPU E5620 @ 2.40GHz Build CPU family: 6 Model: 44 Stepping: 2 Build CPU features: aes apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 C compiler: /usr/bin/x86_64-linux-gnu-gcc GNU gcc-4.8.real (Ubuntu/Linaro 4.8.2-10ubuntu1) 4.8.2 C compiler flags: -msse4.1-Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unused-parameter -Wno-array-bounds -Wno-maybe-uninitialized -Wno-strict-overflow -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG satyabrata@satyabrata-desktop:~$ -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Version problem
tried which mdrun showing the path /usr/bin/mdrun, which v4.6.5, however I have downloaded v5.0.2.tar.gz and used for installation. try to find mdrun program by typing this command on terminal: which mdrun will show path of mdrun program where it located. On Nov 6, 2014 4:01 PM, sa...@physics.iisc.ernet.in wrote: Dear Dr. Carsten Kutzner, I am unable to find the gmx5/bin/GMXRC in my machine, used 'locate' and 'find' to search the location. However I have source the following: source /usr/share/gromacs/shell-specific/GMXRC.bashrc Without this also mdrun is running. I am definitely missing something. Kindly help. With best regards, Satya On 06 Nov 2014, at 07:15, sa...@physics.iisc.ernet.in wrote: Dear all, I am new to GROMACS, just finish installation of v5.0.2, started reading online manual, as instructed executed the command: mdrun -version and the printout pasted below. It is printing GROMACS version 4.6.5, however I have installed version 5.0.2. What is the problem? Find the directory to where you have installed your GROMACS 5.0 executables and then do source /path/to/gmx5/bin/GMXRC which mdrun should now give you the 5.0 mdrun Carsten Regards, Satyabrata Das == Program: mdrun Gromacs version:VERSION 4.6.5 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled GPU support:disabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: SSE4.1 FFT library:fftw-3.3.3-sse2-avx Large file support: enabled RDTSCP usage: enabled Built on: Sun Dec 15 04:01:11 UTC 2013 Built by: buildd@panlong [CMAKE] Build OS/arch: Linux 3.2.0-37-generic x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Xeon(R) CPU E5620 @ 2.40GHz Build CPU family: 6 Model: 44 Stepping: 2 Build CPU features: aes apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 C compiler: /usr/bin/x86_64-linux-gnu-gcc GNU gcc-4.8.real (Ubuntu/Linaro 4.8.2-10ubuntu1) 4.8.2 C compiler flags: -msse4.1-Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unused-parameter -Wno-array-bounds -Wno-maybe-uninitialized -Wno-strict-overflow -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG satyabrata@satyabrata-desktop:~$ -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner
[gmx-users] Minimization is not running
Dear all, I am just new to GROMACS, tried to install v5.0.2, although isntallation was successful, while running it is giving problem: I am just trying to do the lysozyme tutorial, however first energy minimization is not running, mdrun stopped with: === Reading file em.tpr, VERSION 4.6.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads Compiled acceleration: SSE4.1 (Gromacs could use SSE2 on this machine, which is better) Back Off! I just backed up em.trr to ./#em.trr.1# Back Off! I just backed up em.edr to ./#em.edr.1# Illegal instruction (core dumped) I have attached log file which shows during installation compiler flag SSE4.1 was used instead of SSE2, how to fix this? With best regards, Satyabrata Das -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] (no subject)
-- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Version problem
Dear all, I am new to GROMACS, just finish installation of v5.0.2, started reading online manual, as instructed executed the command: mdrun -version and the printout pasted below. It is printing GROMACS version 4.6.5, however I have installed version 5.0.2. What is the problem? Regards, Satyabrata Das == Program: mdrun Gromacs version:VERSION 4.6.5 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled GPU support:disabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: SSE4.1 FFT library:fftw-3.3.3-sse2-avx Large file support: enabled RDTSCP usage: enabled Built on: Sun Dec 15 04:01:11 UTC 2013 Built by: buildd@panlong [CMAKE] Build OS/arch: Linux 3.2.0-37-generic x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Xeon(R) CPU E5620 @ 2.40GHz Build CPU family: 6 Model: 44 Stepping: 2 Build CPU features: aes apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 C compiler: /usr/bin/x86_64-linux-gnu-gcc GNU gcc-4.8.real (Ubuntu/Linaro 4.8.2-10ubuntu1) 4.8.2 C compiler flags: -msse4.1-Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unused-parameter -Wno-array-bounds -Wno-maybe-uninitialized -Wno-strict-overflow -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG satyabrata@satyabrata-desktop:~$ -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
