Re: [gmx-users] Gromacs in UBUNTU
I am still not clear because pdb2gmx_mpi, editconf_mpi commands are working very well. Although they have mpi suffix but its working as non-MPI. Do I have to re-run with (DGMX_MPI=OFF -DGMX_DEFAULT_SUFFIX=OFF ) to get gmx solvate command ... Kindly explain. On 18 May 2015 at 20:39, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, These are not the installation steps you said you followed. Those previous instructions were for a non-MPI build. You've done an MPI build, which explains all your problems. Please be precise ;-) On Mon, May 18, 2015 at 3:55 PM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: definitely yes.. Then only I came to know about this gmx solvant... else How could I? I don't know. The tool is called gmx solvate. my installation steps are follwoing - -- # tar xfz gromacs-5.0.4.tar.gz # cd gromacs-5.0.4 # mkdir build # cd build #sudo CMAKE_PREFIX_PATH=/soft/fftw333/lib cmake .. -DFFTWF_INCLUDE_DIR=/soft/fftw333/include -DFFTWF_LIBRARIES=/soft/fftw333/lib/libfftw3.so -DCMAKE_INSTALL_PREFIX=/soft/gmx504 -DGMX_X11=OFF -DCMAKE_CXX_COMPILER=/usr/bin/mpicxx -DCMAKE_C_COMPILER=/usr/bin/mpicc -DGMX_MPI=ON -DGMX_DOUBLE=OFF -DGMX_DEFAULT_SUFFIX=ON -DGMX_PREFER_STATIC_LIBS=ON You have only installed an MPI build, where gmx gets suffixed to gmx_mpi. If you want the non-MPI tools (which is normal, since only mdrun works with MPI), make and install a non-MPI build. Mark # sudo make # sudo make install # sudo make install-mdrun # source /usr/local/gromacs/bin/GMXRC # ls /soft/gmx504/bin/ demux.pl g_density_mpi g_gyrate_mpi GMXRC.bash g_rms_mpi g_tune_pme_mpi do_dssp_mpi g_densmap_mpi g_h2order_mpi GMXRC.cshgrompp_mpi g_vanhove_mpi editconf_mpi g_densorder_mpi g_hbond_mpi GMXRC.zshg_rotacf_mpi g_velacc_mpi eneconv_mpi g_dielectric_mpi g_helix_mpi g_nmeig_mpi g_rotmat_mpi g_wham_mpi g_anadock_mpig_dipoles_mpi g_helixorient_mpi g_nmens_mpi g_saltbr_mpi g_wheel_mpi g_anaeig_mpi g_disre_mpi g_hydorder_mpi g_nmtraj_mpi g_sans_mpi g_x2top_mpi g_analyze_mpig_dist_mpig_lie_mpi g_options_mpig_sas_mpi make_edi_mpi g_angle_mpi g_dos_mpi g_mdmat_mpi g_order_mpi g_saxs_mpi make_ndx_mpi g_bar_mpig_dyecoupl_mpig_mindist_mpi g_pme_error_mpi g_select_mpi mdrun_mpi g_bond_mpi g_dyndom_mpi g_morph_mpi g_polystat_mpi g_sgangle_mpi mk_angndx_mpi g_bundle_mpi genbox_mpig_msd_mpi g_potential_mpi g_sham_mpi pdb2gmx_mpi g_chi_mpigenconf_mpi gmxcheck_mpi g_principal_mpi g_sigeps_mpi tpbconv_mpi g_cluster_mpig_enemat_mpi gmx-completion.bash g_protonate_mpi g_sorient_mpi trjcat_mpi g_clustsize_mpi g_energy_mpi gmx-completion-gmx_mpi.bash g_rama_mpi g_spatial_mpi trjconv_mpi g_confrms_mpigenion_mpigmxdump_mpi g_rdf_mpig_spol_mpi trjorder_mpi g_covar_mpi genrestr_mpi gmx_mpi g_rmsdist_mpig_tcaf_mpi xplor2gmx.pl g_current_mpig_filter_mpi GMXRC g_rmsf_mpi g_traj_mpi xpm2ps_mpi which doesn't have that gmx commands On 18 May 2015 at 17:40, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Did you go and read the webpage that is suggested by the rest of that message? Mark On Mon, May 18, 2015 at 12:57 PM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: sorry.. I mean pdb2gmx, editconf, genion, grompp and mdrun even it has genbox but it says This tool has been removed from Gromacs 5.0. On 18 May 2015 at 15:38, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, What other commands are working? Please be specific, we don't have time to spend on guesses :-) Mark On Mon, 18 May 2015 11:06 Sanchaita Rajkhowa srajkhow...@gmail.com wrote: Hi actually all other commands are working fine. only when I am runing: -- g@chandan:~$ gmx solvate -cp protein.pdb -cs tip4p.gro -p topol.top -o solv.pdb No command 'gmx' found, did you mean: Command 'gm' from package 'graphicsmagick' (universe) Command 'gcx' from package 'gcx' (universe) Command 'gmt' from package 'libgenome-perl' (universe) Command 'ngmx' from package 'gromacs' (universe) gmx: command not found --- this error is coming. gmx solvant doesn't exist, of course, but I assume that was a typo! I have all options but its not working and even it doesn't show like other commands in the installation dir /soft/gmx504/bin/ what else to try!!
Re: [gmx-users] Gromacs in UBUNTU
Hi, Use gmx_mpi solvate. You can get away with using pdb2gmx_mpi in GROMACS 5 just like old GROMACS versions only because those are magically transformed into things like gmx_mpi pdb2gmx, to provide a year of backwards compatibility. But providing backwards compatibility for a new name was not really a good thing to do, so there is no solvate_mpi. GROMACS 5.1 will remove the old-style names without gmx prefixes, so people need to start getting used to using the gmx prefix (or learn to roll their own symlinks). Mark On Mon, May 18, 2015 at 5:19 PM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: I am still not clear because pdb2gmx_mpi, editconf_mpi commands are working very well. Although they have mpi suffix but its working as non-MPI. Do I have to re-run with (DGMX_MPI=OFF -DGMX_DEFAULT_SUFFIX=OFF ) to get gmx solvate command ... Kindly explain. On 18 May 2015 at 20:39, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, These are not the installation steps you said you followed. Those previous instructions were for a non-MPI build. You've done an MPI build, which explains all your problems. Please be precise ;-) On Mon, May 18, 2015 at 3:55 PM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: definitely yes.. Then only I came to know about this gmx solvant... else How could I? I don't know. The tool is called gmx solvate. my installation steps are follwoing - -- # tar xfz gromacs-5.0.4.tar.gz # cd gromacs-5.0.4 # mkdir build # cd build #sudo CMAKE_PREFIX_PATH=/soft/fftw333/lib cmake .. -DFFTWF_INCLUDE_DIR=/soft/fftw333/include -DFFTWF_LIBRARIES=/soft/fftw333/lib/libfftw3.so -DCMAKE_INSTALL_PREFIX=/soft/gmx504 -DGMX_X11=OFF -DCMAKE_CXX_COMPILER=/usr/bin/mpicxx -DCMAKE_C_COMPILER=/usr/bin/mpicc -DGMX_MPI=ON -DGMX_DOUBLE=OFF -DGMX_DEFAULT_SUFFIX=ON -DGMX_PREFER_STATIC_LIBS=ON You have only installed an MPI build, where gmx gets suffixed to gmx_mpi. If you want the non-MPI tools (which is normal, since only mdrun works with MPI), make and install a non-MPI build. Mark # sudo make # sudo make install # sudo make install-mdrun # source /usr/local/gromacs/bin/GMXRC # ls /soft/gmx504/bin/ demux.pl g_density_mpi g_gyrate_mpi GMXRC.bash g_rms_mpi g_tune_pme_mpi do_dssp_mpi g_densmap_mpi g_h2order_mpi GMXRC.cshgrompp_mpi g_vanhove_mpi editconf_mpi g_densorder_mpi g_hbond_mpi GMXRC.zshg_rotacf_mpi g_velacc_mpi eneconv_mpi g_dielectric_mpi g_helix_mpi g_nmeig_mpi g_rotmat_mpi g_wham_mpi g_anadock_mpig_dipoles_mpi g_helixorient_mpi g_nmens_mpi g_saltbr_mpi g_wheel_mpi g_anaeig_mpi g_disre_mpi g_hydorder_mpi g_nmtraj_mpi g_sans_mpi g_x2top_mpi g_analyze_mpig_dist_mpig_lie_mpi g_options_mpig_sas_mpi make_edi_mpi g_angle_mpi g_dos_mpi g_mdmat_mpi g_order_mpi g_saxs_mpi make_ndx_mpi g_bar_mpig_dyecoupl_mpig_mindist_mpi g_pme_error_mpi g_select_mpi mdrun_mpi g_bond_mpi g_dyndom_mpi g_morph_mpi g_polystat_mpi g_sgangle_mpi mk_angndx_mpi g_bundle_mpi genbox_mpig_msd_mpi g_potential_mpi g_sham_mpi pdb2gmx_mpi g_chi_mpigenconf_mpi gmxcheck_mpi g_principal_mpi g_sigeps_mpi tpbconv_mpi g_cluster_mpig_enemat_mpi gmx-completion.bash g_protonate_mpi g_sorient_mpi trjcat_mpi g_clustsize_mpi g_energy_mpi gmx-completion-gmx_mpi.bash g_rama_mpi g_spatial_mpi trjconv_mpi g_confrms_mpigenion_mpigmxdump_mpi g_rdf_mpig_spol_mpi trjorder_mpi g_covar_mpi genrestr_mpi gmx_mpi g_rmsdist_mpig_tcaf_mpi xplor2gmx.pl g_current_mpig_filter_mpi GMXRC g_rmsf_mpi g_traj_mpi xpm2ps_mpi which doesn't have that gmx commands On 18 May 2015 at 17:40, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Did you go and read the webpage that is suggested by the rest of that message? Mark On Mon, May 18, 2015 at 12:57 PM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: sorry.. I mean pdb2gmx, editconf, genion, grompp and mdrun even it has genbox but it says This tool has been removed from Gromacs 5.0. On 18 May 2015 at 15:38, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, What other commands are working? Please be specific, we don't have time to spend on guesses :-) Mark On Mon, 18 May 2015 11:06 Sanchaita Rajkhowa srajkhow...@gmail.com wrote: Hi actually all other commands are working fine. only when I am runing: -- g@chandan:~$ gmx solvate -cp protein.pdb -cs
Re: [gmx-users] Gromacs in UBUNTU
Hi, These are not the installation steps you said you followed. Those previous instructions were for a non-MPI build. You've done an MPI build, which explains all your problems. Please be precise ;-) On Mon, May 18, 2015 at 3:55 PM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: definitely yes.. Then only I came to know about this gmx solvant... else How could I? I don't know. The tool is called gmx solvate. my installation steps are follwoing - -- # tar xfz gromacs-5.0.4.tar.gz # cd gromacs-5.0.4 # mkdir build # cd build #sudo CMAKE_PREFIX_PATH=/soft/fftw333/lib cmake .. -DFFTWF_INCLUDE_DIR=/soft/fftw333/include -DFFTWF_LIBRARIES=/soft/fftw333/lib/libfftw3.so -DCMAKE_INSTALL_PREFIX=/soft/gmx504 -DGMX_X11=OFF -DCMAKE_CXX_COMPILER=/usr/bin/mpicxx -DCMAKE_C_COMPILER=/usr/bin/mpicc -DGMX_MPI=ON -DGMX_DOUBLE=OFF -DGMX_DEFAULT_SUFFIX=ON -DGMX_PREFER_STATIC_LIBS=ON You have only installed an MPI build, where gmx gets suffixed to gmx_mpi. If you want the non-MPI tools (which is normal, since only mdrun works with MPI), make and install a non-MPI build. Mark # sudo make # sudo make install # sudo make install-mdrun # source /usr/local/gromacs/bin/GMXRC # ls /soft/gmx504/bin/ demux.pl g_density_mpi g_gyrate_mpi GMXRC.bash g_rms_mpi g_tune_pme_mpi do_dssp_mpi g_densmap_mpi g_h2order_mpi GMXRC.cshgrompp_mpi g_vanhove_mpi editconf_mpi g_densorder_mpi g_hbond_mpi GMXRC.zshg_rotacf_mpi g_velacc_mpi eneconv_mpi g_dielectric_mpi g_helix_mpi g_nmeig_mpi g_rotmat_mpi g_wham_mpi g_anadock_mpig_dipoles_mpi g_helixorient_mpi g_nmens_mpi g_saltbr_mpi g_wheel_mpi g_anaeig_mpi g_disre_mpi g_hydorder_mpi g_nmtraj_mpi g_sans_mpi g_x2top_mpi g_analyze_mpig_dist_mpig_lie_mpi g_options_mpig_sas_mpi make_edi_mpi g_angle_mpi g_dos_mpi g_mdmat_mpi g_order_mpi g_saxs_mpi make_ndx_mpi g_bar_mpig_dyecoupl_mpig_mindist_mpi g_pme_error_mpi g_select_mpi mdrun_mpi g_bond_mpi g_dyndom_mpi g_morph_mpi g_polystat_mpi g_sgangle_mpi mk_angndx_mpi g_bundle_mpi genbox_mpig_msd_mpi g_potential_mpi g_sham_mpi pdb2gmx_mpi g_chi_mpigenconf_mpi gmxcheck_mpi g_principal_mpi g_sigeps_mpi tpbconv_mpi g_cluster_mpig_enemat_mpi gmx-completion.bash g_protonate_mpi g_sorient_mpi trjcat_mpi g_clustsize_mpi g_energy_mpi gmx-completion-gmx_mpi.bash g_rama_mpi g_spatial_mpi trjconv_mpi g_confrms_mpigenion_mpigmxdump_mpi g_rdf_mpig_spol_mpi trjorder_mpi g_covar_mpi genrestr_mpi gmx_mpi g_rmsdist_mpig_tcaf_mpi xplor2gmx.pl g_current_mpig_filter_mpi GMXRC g_rmsf_mpi g_traj_mpi xpm2ps_mpi which doesn't have that gmx commands On 18 May 2015 at 17:40, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Did you go and read the webpage that is suggested by the rest of that message? Mark On Mon, May 18, 2015 at 12:57 PM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: sorry.. I mean pdb2gmx, editconf, genion, grompp and mdrun even it has genbox but it says This tool has been removed from Gromacs 5.0. On 18 May 2015 at 15:38, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, What other commands are working? Please be specific, we don't have time to spend on guesses :-) Mark On Mon, 18 May 2015 11:06 Sanchaita Rajkhowa srajkhow...@gmail.com wrote: Hi actually all other commands are working fine. only when I am runing: -- g@chandan:~$ gmx solvate -cp protein.pdb -cs tip4p.gro -p topol.top -o solv.pdb No command 'gmx' found, did you mean: Command 'gm' from package 'graphicsmagick' (universe) Command 'gcx' from package 'gcx' (universe) Command 'gmt' from package 'libgenome-perl' (universe) Command 'ngmx' from package 'gromacs' (universe) gmx: command not found --- this error is coming. gmx solvant doesn't exist, of course, but I assume that was a typo! I have all options but its not working and even it doesn't show like other commands in the installation dir /soft/gmx504/bin/ what else to try!! On 18 May 2015 at 13:11, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, You may need to give your normal user account read permission to that directory. gmx solvant doesn't exist, of course, but I assume that was a typo! :-) Mark On Mon, May 18, 2015 at 6:58 AM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: Dear all I followed the same steps to install Gromacs -
Re: [gmx-users] position resrtraints
Dear Justin, thanka 4 ur prompt reply. I checked that there was another issue. I didnot modify the aminoacids.rtp file in order to incorporate the new graphene.pdb atom types according to the force field. It appears to me that the correct interaction is not arsising because the atoms mentioned in the PDB file is alien to the force field. Is it the case? Should I modify the aminoacids .rtp file to account for the sp2 carbon atoms and the terminal hydrogens mentioned in the PDB file and then procced without really bothering about pdb2gmx and position restraints? I think I made a very silly mistake to begin with. Your help, as always will be appreciated. Regards, Soumadwip Research Fellow IIT Bombay India -- 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] Best way/utility to convert .xtc to .dcd
Hello All, What is the best way/utility available to convert GROMACS .xtc to a CHARMM .dcd. I have tried CATDCD but I am not getting a desired outcome. Kindly help. Thanks, sxn -- 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] Implementing an angle-dependent potential
Hi all, I am trying to add hydrogen bonds to a coarse grained protein model by Ali Ghavami. The model has one bead per amino acid placed at each C-alpha. The model has bending and torsion potentials, and also includes non-bonded interactions like hydrophobicity and electrostatic interactions. (Some beads have charges). For the hydrogen bonds, the best thing would be to use a directional potential, i.e. the interaction would depend not only on distance, but also on the orientation of both C-alpha's. I was not able to find such a potential for non-bonded interactions in GROMACS however. Does anyone know a way to accomplish this in GROMACS? Any help would be welcome. Wopke -- 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] Gromacs in UBUNTU
Hi, Did you go and read the webpage that is suggested by the rest of that message? Mark On Mon, May 18, 2015 at 12:57 PM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: sorry.. I mean pdb2gmx, editconf, genion, grompp and mdrun even it has genbox but it says This tool has been removed from Gromacs 5.0. On 18 May 2015 at 15:38, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, What other commands are working? Please be specific, we don't have time to spend on guesses :-) Mark On Mon, 18 May 2015 11:06 Sanchaita Rajkhowa srajkhow...@gmail.com wrote: Hi actually all other commands are working fine. only when I am runing: -- g@chandan:~$ gmx solvate -cp protein.pdb -cs tip4p.gro -p topol.top -o solv.pdb No command 'gmx' found, did you mean: Command 'gm' from package 'graphicsmagick' (universe) Command 'gcx' from package 'gcx' (universe) Command 'gmt' from package 'libgenome-perl' (universe) Command 'ngmx' from package 'gromacs' (universe) gmx: command not found --- this error is coming. gmx solvant doesn't exist, of course, but I assume that was a typo! I have all options but its not working and even it doesn't show like other commands in the installation dir /soft/gmx504/bin/ what else to try!! On 18 May 2015 at 13:11, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, You may need to give your normal user account read permission to that directory. gmx solvant doesn't exist, of course, but I assume that was a typo! :-) Mark On Mon, May 18, 2015 at 6:58 AM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: Dear all I followed the same steps to install Gromacs - 5.0.4 in ubuntu - 14.04 (64bit) and seems like things get installed but I am not able to get gmx solvant command. I have searched in my installation dir /soft/gmx504/bin/ and also source /soft/gmx504/bin/GMXRC.bash in my bashrc file. Kindly help. with regards Sanchaita On 14 May 2015 at 08:54, James Lord jjamesgreen...@gmail.com wrote: Hi Saeed, You don't necessarily need to install it first from Ubuntu software center and then update it. you can directly get the latest version and follow the instruction on gromacs website. Quick and dirty installation http://www.gromacs.org/Documentation/Installation_Instructions_5.0?highlight=command#TOC 1. Get the latest version of your C and C++ compilers. 2. Check that you have CMake version 2.8.8 or later. 3. Get and unpack the latest version of the GROMACS tarball. 4. Make a separate build directory and change to it. 5. Run cmake with the path to the source as an argument 6. Run make, make check, and make install Or, as a sequence of commands to execute: tar xfz gromacs-5.0.5.tar.gz cd gromacs-5.0.5 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON make make check sudo make install source /usr/local/gromacs/bin/GMXRC Cheers James On Thu, May 14, 2015 at 1:53 PM, saeed poorasad s_poora...@yahoo.com wrote: Dear Gromacs users , Greetings .I want to install Gromacs with using of UBUNTU software center . Now I want to know about updating process of this version of gromacs . Does it update automatically with Ubuntu ? Thanks for your attention .Best,Saeed. -- 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. -- 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
Re: [gmx-users] Gromacs in UBUNTU
definitely yes.. Then only I came to know about this gmx solvant... else How could I? my installation steps are follwoing - -- # tar xfz gromacs-5.0.4.tar.gz # cd gromacs-5.0.4 # mkdir build # cd build #sudo CMAKE_PREFIX_PATH=/soft/fftw333/lib cmake .. -DFFTWF_INCLUDE_DIR=/soft/fftw333/include -DFFTWF_LIBRARIES=/soft/fftw333/lib/libfftw3.so -DCMAKE_INSTALL_PREFIX=/soft/gmx504 -DGMX_X11=OFF -DCMAKE_CXX_COMPILER=/usr/bin/mpicxx -DCMAKE_C_COMPILER=/usr/bin/mpicc -DGMX_MPI=ON -DGMX_DOUBLE=OFF -DGMX_DEFAULT_SUFFIX=ON -DGMX_PREFER_STATIC_LIBS=ON # sudo make # sudo make install # sudo make install-mdrun # source /usr/local/gromacs/bin/GMXRC # ls /soft/gmx504/bin/ demux.pl g_density_mpi g_gyrate_mpi GMXRC.bash g_rms_mpi g_tune_pme_mpi do_dssp_mpi g_densmap_mpi g_h2order_mpi GMXRC.cshgrompp_mpi g_vanhove_mpi editconf_mpi g_densorder_mpi g_hbond_mpi GMXRC.zshg_rotacf_mpi g_velacc_mpi eneconv_mpi g_dielectric_mpi g_helix_mpi g_nmeig_mpi g_rotmat_mpi g_wham_mpi g_anadock_mpig_dipoles_mpi g_helixorient_mpi g_nmens_mpi g_saltbr_mpi g_wheel_mpi g_anaeig_mpi g_disre_mpi g_hydorder_mpi g_nmtraj_mpi g_sans_mpi g_x2top_mpi g_analyze_mpig_dist_mpig_lie_mpi g_options_mpig_sas_mpi make_edi_mpi g_angle_mpi g_dos_mpi g_mdmat_mpi g_order_mpi g_saxs_mpi make_ndx_mpi g_bar_mpig_dyecoupl_mpig_mindist_mpi g_pme_error_mpi g_select_mpi mdrun_mpi g_bond_mpi g_dyndom_mpi g_morph_mpi g_polystat_mpi g_sgangle_mpi mk_angndx_mpi g_bundle_mpi genbox_mpig_msd_mpi g_potential_mpi g_sham_mpi pdb2gmx_mpi g_chi_mpigenconf_mpi gmxcheck_mpi g_principal_mpi g_sigeps_mpi tpbconv_mpi g_cluster_mpig_enemat_mpi gmx-completion.bash g_protonate_mpi g_sorient_mpi trjcat_mpi g_clustsize_mpi g_energy_mpi gmx-completion-gmx_mpi.bash g_rama_mpi g_spatial_mpi trjconv_mpi g_confrms_mpigenion_mpigmxdump_mpi g_rdf_mpig_spol_mpi trjorder_mpi g_covar_mpi genrestr_mpi gmx_mpi g_rmsdist_mpig_tcaf_mpi xplor2gmx.pl g_current_mpig_filter_mpi GMXRC g_rmsf_mpi g_traj_mpi xpm2ps_mpi which doesn't have that gmx commands On 18 May 2015 at 17:40, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Did you go and read the webpage that is suggested by the rest of that message? Mark On Mon, May 18, 2015 at 12:57 PM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: sorry.. I mean pdb2gmx, editconf, genion, grompp and mdrun even it has genbox but it says This tool has been removed from Gromacs 5.0. On 18 May 2015 at 15:38, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, What other commands are working? Please be specific, we don't have time to spend on guesses :-) Mark On Mon, 18 May 2015 11:06 Sanchaita Rajkhowa srajkhow...@gmail.com wrote: Hi actually all other commands are working fine. only when I am runing: -- g@chandan:~$ gmx solvate -cp protein.pdb -cs tip4p.gro -p topol.top -o solv.pdb No command 'gmx' found, did you mean: Command 'gm' from package 'graphicsmagick' (universe) Command 'gcx' from package 'gcx' (universe) Command 'gmt' from package 'libgenome-perl' (universe) Command 'ngmx' from package 'gromacs' (universe) gmx: command not found --- this error is coming. gmx solvant doesn't exist, of course, but I assume that was a typo! I have all options but its not working and even it doesn't show like other commands in the installation dir /soft/gmx504/bin/ what else to try!! On 18 May 2015 at 13:11, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, You may need to give your normal user account read permission to that directory. gmx solvant doesn't exist, of course, but I assume that was a typo! :-) Mark On Mon, May 18, 2015 at 6:58 AM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: Dear all I followed the same steps to install Gromacs - 5.0.4 in ubuntu - 14.04 (64bit) and seems like things get installed but I am not able to get gmx solvant command. I have searched in my installation dir /soft/gmx504/bin/ and also source /soft/gmx504/bin/GMXRC.bash in my bashrc file. Kindly help. with regards Sanchaita On 14 May 2015 at 08:54, James Lord jjamesgreen...@gmail.com wrote: Hi Saeed, You don't necessarily need to install it first from Ubuntu software center and then update it. you can directly get the latest version and follow the instruction on gromacs website.
Re: [gmx-users] first residue in chains warning issue
On 5/18/15 7:53 AM, Ming Tang wrote: Hi Justin, Do you mean options for bonds or something like fix and pull atoms? From the error... Maybe you forgot to change the constraints mdp option. -Justin -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Monday, 18 May 2015 9:44 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] first residue in chains warning issue On 5/18/15 7:39 AM, Ming Tang wrote: Dear Justin, After minimization, I got the following note when using NPT. NOTE 1 [file topol.top, line 49]: The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has an estimated oscillational period of 1.0e-02 ps, which is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change the constraints mdp option. Does this has something to do with the warning given by pdb2gmx? When reducing dt from 0.001ps to 0.0009ps, the note is gone. Is there anything wrong with my topol.top? No, as the note says, you probably aren't using constraints, which if you want a 1-fs or larger value of dt, you need to be using. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] first residue in chains warning issue
Hi Justin, Do you mean options for bonds or something like fix and pull atoms? -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Monday, 18 May 2015 9:44 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] first residue in chains warning issue On 5/18/15 7:39 AM, Ming Tang wrote: Dear Justin, After minimization, I got the following note when using NPT. NOTE 1 [file topol.top, line 49]: The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has an estimated oscillational period of 1.0e-02 ps, which is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change the constraints mdp option. Does this has something to do with the warning given by pdb2gmx? When reducing dt from 0.001ps to 0.0009ps, the note is gone. Is there anything wrong with my topol.top? No, as the note says, you probably aren't using constraints, which if you want a 1-fs or larger value of dt, you need to be using. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
Re: [gmx-users] energy minimization problem
Hi Tsjerk, I just tried, but it stopped for too many LICS warnings at step 6000. Small triple helix can be equilibrated for 1000ns with NPT. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Monday, 18 May 2015 6:21 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] energy minimization problem Hi Ming Tang, Can you run in NVT? Then afterwards you can try NPT without position restraints. Cheers, Tsjerk On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote: Thanks a lot, Justin It really makes me feel weird. The small triple helix with 30 amino acids per chain(generated simply by deleting other atoms in .pdb file of the real triple helix) can be equilibrated for 1ns using exactly the same control files, and the real triple helix can be used for full atomic simulation without any problem. The CG topology is generated using the same mitinize.py downloaded from the website. I will try for another time, and will tell you if I fix it. Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Sunday, 17 May 2015 7:07 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/16/15 8:30 AM, Ming Tang wrote: Dear Justin, I tried to use small time step. First, set dt=0.005ps, after running 20ps, I found one chain of the triple helix just went to another water box totally. I guess there is something wrong with the martini ff because of the small time step. Then, I increased it to 0.01ps, after running 40ps, I checked the .gro, and found all the three chains stay together, which is reasonable. However, even use dt=0.01, the simulation can only run about 1ns. And, after simulating 100 ps using dt=0.01ps, the simulation can just run thousands of steps when dt is increased to 0.02ps. I tried many times and many different time steps, but still could not see the possibility for it to run hundreds of nanoseconds, which is quite normal when using martini force. If the system can be further minimized, then it can run longer maybe. This seems entirely random and suggests instead that there is something simply physically unstable with the system or problematic in the topology. I don't use MARTINI (or CG models in general) so there's little else I can suggest. Maybe someone more experienced with such systems will chime in. Also note that a chain moving into another box is probably just a PBC effect and not a true dissociation. If it is a dissociation, it's not simply because of the time step. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- 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.
Re: [gmx-users] Gromacs in UBUNTU
Hi, You may need to give your normal user account read permission to that directory. gmx solvant doesn't exist, of course, but I assume that was a typo! :-) Mark On Mon, May 18, 2015 at 6:58 AM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: Dear all I followed the same steps to install Gromacs - 5.0.4 in ubuntu - 14.04 (64bit) and seems like things get installed but I am not able to get gmx solvant command. I have searched in my installation dir /soft/gmx504/bin/ and also source /soft/gmx504/bin/GMXRC.bash in my bashrc file. Kindly help. with regards Sanchaita On 14 May 2015 at 08:54, James Lord jjamesgreen...@gmail.com wrote: Hi Saeed, You don't necessarily need to install it first from Ubuntu software center and then update it. you can directly get the latest version and follow the instruction on gromacs website. Quick and dirty installation http://www.gromacs.org/Documentation/Installation_Instructions_5.0?highlight=command#TOC 1. Get the latest version of your C and C++ compilers. 2. Check that you have CMake version 2.8.8 or later. 3. Get and unpack the latest version of the GROMACS tarball. 4. Make a separate build directory and change to it. 5. Run cmake with the path to the source as an argument 6. Run make, make check, and make install Or, as a sequence of commands to execute: tar xfz gromacs-5.0.5.tar.gz cd gromacs-5.0.5 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON make make check sudo make install source /usr/local/gromacs/bin/GMXRC Cheers James On Thu, May 14, 2015 at 1:53 PM, saeed poorasad s_poora...@yahoo.com wrote: Dear Gromacs users , Greetings .I want to install Gromacs with using of UBUNTU software center . Now I want to know about updating process of this version of gromacs . Does it update automatically with Ubuntu ? Thanks for your attention .Best,Saeed. -- 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. -- 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.
Re: [gmx-users] warter freeze into ice when cutoff-scheme=Verlet and coulombtype = cut-off
Hi, That behaviour might depend on what your starting configuration is, e.g. what group MOL has frozen coordinates. But cut-off is anyway a ~useless model for condensed phase of atoms with partial charges, so understanding the issue hasn't got much value. Mark On Mon, May 18, 2015 at 3:58 AM niexuechuan niexuech...@126.com wrote: Hi everyone, I found that after gromacs version 4.6, when set cutoff-scheme=Verlet and coulombtype= cut-off, the waters in the system will freeze into ice. I known that charge-groups are necessary when using plain cut-off electrostatics. But I'm surprised that why the waters freeze into ice when using plain cut-off electrostatics without charge-groups? Could someone explain how it happenes? My mdp files are like this: integrator = md constraints = all_bonds dt = 0.002 nsteps = 5000 comm-mode =None nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 25000 nstxtcout= 500 xtc-precision= 1000 energygrps = MOL SOL nstlist = 1 ns_type = grid pbc = xyz rlist= 1.0 coulombtype = cut-off rcoulomb-switch = 0 rcoulomb = 1.0 vdw-type = cut-off rvdw-switch = 0 rvdw = 1.0 Tcoupl = V-rescale nsttcouple = -1 tc-grps = MOLSOL tau_t= 0.10.1 ref_t= 300 300 freezegrps = MOL freezedim= Y Y Y Thanks! Xuechuan -- 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.
Re: [gmx-users] energy minimization problem
Thanks a lot, Justin It really makes me feel weird. The small triple helix with 30 amino acids per chain(generated simply by deleting other atoms in .pdb file of the real triple helix) can be equilibrated for 1ns using exactly the same control files, and the real triple helix can be used for full atomic simulation without any problem. The CG topology is generated using the same mitinize.py downloaded from the website. I will try for another time, and will tell you if I fix it. Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Sunday, 17 May 2015 7:07 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/16/15 8:30 AM, Ming Tang wrote: Dear Justin, I tried to use small time step. First, set dt=0.005ps, after running 20ps, I found one chain of the triple helix just went to another water box totally. I guess there is something wrong with the martini ff because of the small time step. Then, I increased it to 0.01ps, after running 40ps, I checked the .gro, and found all the three chains stay together, which is reasonable. However, even use dt=0.01, the simulation can only run about 1ns. And, after simulating 100 ps using dt=0.01ps, the simulation can just run thousands of steps when dt is increased to 0.02ps. I tried many times and many different time steps, but still could not see the possibility for it to run hundreds of nanoseconds, which is quite normal when using martini force. If the system can be further minimized, then it can run longer maybe. This seems entirely random and suggests instead that there is something simply physically unstable with the system or problematic in the topology. I don't use MARTINI (or CG models in general) so there's little else I can suggest. Maybe someone more experienced with such systems will chime in. Also note that a chain moving into another box is probably just a PBC effect and not a true dissociation. If it is a dissociation, it's not simply because of the time step. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
Re: [gmx-users] energy minimization problem
Hi Ming Tang, Can you run in NVT? Then afterwards you can try NPT without position restraints. Cheers, Tsjerk On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote: Thanks a lot, Justin It really makes me feel weird. The small triple helix with 30 amino acids per chain(generated simply by deleting other atoms in .pdb file of the real triple helix) can be equilibrated for 1ns using exactly the same control files, and the real triple helix can be used for full atomic simulation without any problem. The CG topology is generated using the same mitinize.py downloaded from the website. I will try for another time, and will tell you if I fix it. Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Sunday, 17 May 2015 7:07 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/16/15 8:30 AM, Ming Tang wrote: Dear Justin, I tried to use small time step. First, set dt=0.005ps, after running 20ps, I found one chain of the triple helix just went to another water box totally. I guess there is something wrong with the martini ff because of the small time step. Then, I increased it to 0.01ps, after running 40ps, I checked the .gro, and found all the three chains stay together, which is reasonable. However, even use dt=0.01, the simulation can only run about 1ns. And, after simulating 100 ps using dt=0.01ps, the simulation can just run thousands of steps when dt is increased to 0.02ps. I tried many times and many different time steps, but still could not see the possibility for it to run hundreds of nanoseconds, which is quite normal when using martini force. If the system can be further minimized, then it can run longer maybe. This seems entirely random and suggests instead that there is something simply physically unstable with the system or problematic in the topology. I don't use MARTINI (or CG models in general) so there's little else I can suggest. Maybe someone more experienced with such systems will chime in. Also note that a chain moving into another box is probably just a PBC effect and not a true dissociation. If it is a dissociation, it's not simply because of the time step. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- 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] normal mode analysis and system size ...
hi , I've been trying to perform a nromal mode analysis using (after a thorough energy minimization of my system) prompt mdrun_d -v -s nm.tpr -o nm.trr -mtx nm.mtx[...] Maximum force: 8.56366e+00 The force is probably not small enough to ensure that you are at a minimum. Be aware that negative eigenvalues may occur when the resulting matrix is diagonalized.Finished step 9060 out of 9060 Writing Hessian... i ignored the warning hoping to get a away with that ... then: prompt gmx nmeig -f nm.mtx -s nm.tpr -v nmeig.trr [...] Reading double precision matrix generated by Gromacs VERSION 5.0.4 Full matrix storage format, nrow=27180, ncols=27180 Diagonalizing to find vectors 1 through 50... and at this point it has been working for something like three days now and still going ...my system (a sample of a small organic molecule glass) has about 1 atoms(including protons) ... can anybody give me an estimate of what kind of system sizeis feasible for this kind of calculation? or could it be that gmx nmeig gets stuck (withoutwarning) when it encounters negative eigenvalues? thanks,michael ===Why be happy when you could be normal? -- 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] energy minimization problem
Hi Ming Tang, That's pretty quick. I guess that this is on multiple cores, given the size of the system. It often helps to equilibrate on a limited number of cores, but I'm not sure that's feasible. Did you obtain the model by martinizing the original structure, or did you use the relaxed structure from the atomistic simulation? How did you solvate the system? Cheers, Tsjerk On May 18, 2015 10:29, Ming Tang m21.t...@qut.edu.au wrote: Hi Tsjerk, I just tried, but it stopped for too many LICS warnings at step 6000. Small triple helix can be equilibrated for 1000ns with NPT. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Monday, 18 May 2015 6:21 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] energy minimization problem Hi Ming Tang, Can you run in NVT? Then afterwards you can try NPT without position restraints. Cheers, Tsjerk On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote: Thanks a lot, Justin It really makes me feel weird. The small triple helix with 30 amino acids per chain(generated simply by deleting other atoms in .pdb file of the real triple helix) can be equilibrated for 1ns using exactly the same control files, and the real triple helix can be used for full atomic simulation without any problem. The CG topology is generated using the same mitinize.py downloaded from the website. I will try for another time, and will tell you if I fix it. Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Sunday, 17 May 2015 7:07 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/16/15 8:30 AM, Ming Tang wrote: Dear Justin, I tried to use small time step. First, set dt=0.005ps, after running 20ps, I found one chain of the triple helix just went to another water box totally. I guess there is something wrong with the martini ff because of the small time step. Then, I increased it to 0.01ps, after running 40ps, I checked the .gro, and found all the three chains stay together, which is reasonable. However, even use dt=0.01, the simulation can only run about 1ns. And, after simulating 100 ps using dt=0.01ps, the simulation can just run thousands of steps when dt is increased to 0.02ps. I tried many times and many different time steps, but still could not see the possibility for it to run hundreds of nanoseconds, which is quite normal when using martini force. If the system can be further minimized, then it can run longer maybe. This seems entirely random and suggests instead that there is something simply physically unstable with the system or problematic in the topology. I don't use MARTINI (or CG models in general) so there's little else I can suggest. Maybe someone more experienced with such systems will chime in. Also note that a chain moving into another box is probably just a PBC effect and not a true dissociation. If it is a dissociation, it's not simply because of the time step. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- 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
[gmx-users] mdp options for charmm27 force field in gromacs version 4.6.7
Dear Users: I would like to use the charmm27 force field in gromacs version 4.6.7 and I would like to know if it is possible to get the proper treatment of vdw interactions. Information for gromacs 5 is here: http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM However, Gromacs 4.6.7 does not contain the option for vdw-modifier = force-switch Invalid enum 'force-switch' for variable vdw-modifier, using 'Potential-shift-Verlet' Next time use one of: 'Potential-shift-Verlet' 'Potential-shift' 'None' 'Potential-switch' 'Exact-cutoff' Is a potential-shift the same as a force-switch and therefore the following options are correct for charmm27 in gromacs 4.6.7? ns_type = grid cutoff-scheme = verlet vdwtype = cut-off rlist = 1.2 rvdw = 1.2 rvdw-switch = 1.0 rcoulomb = 1.2 vdw-modifier = Potential-shift-Verlet coulombtype = PME I know this has been discussed before on the list, but I can't find anything that seems authoritative for gromacs versions prior to v5. Thank you for your assistance, Chris. -- 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] Protein-Ligand complex Implicit simulation
Hello Everyone, I am trying to do protein-ligand complex simulation with implicit solvent parameters using gromacs. As, ligand parameters are not present in gbsa.itp, I added all the possible atomtypes and their van der wall radii from gaff ff and also managed to get get the HCT paremeters. Still its giving errorsAnyone please suggest me how to proceed further. Thanks in Advance -- -- SUNITA GUPTA Senior Research Fellow Bioinformatics Centre Jawaharlal Nehru University New Delhi- 110067 Email- sunita@gmail.com -- 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] question
Dear Mark
I installed the newest version of cmake (3.2.2).
After using cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
CUDA_TOOLKIT_ROOT_DIR not found or specified
-- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR
CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY) (Required is at
least version 4.0)
-- No compatible CUDA toolkit found (v4.0+), disabling native GPU
acceleration
-- The GROMACS-managed build of FFTW 3 will configure with the following
optimizations: --enable-sse2
Downloading: http://gerrit.gromacs.org/download/regressiontests-5.0.5.tar.gz
-- [download 100% complete]
CMake Error at tests/CMakeLists.txt:57 (message):
error: downloading
'http://gerrit.gromacs.org/download/regressiontests-5.0.5.tar.gz' failed
status_code: 1
status_string: Unsupported protocol
log: Hostname was NOT found in DNS cache
Trying 130.237.25.133...
Connected to gerrit.gromacs.org (130.237.25.133) port 80 (#0)
GET /download/regressiontests-5.0.5.tar.gz HTTP/1.1
User-Agent: curl/7.38.0
Host: gerrit.gromacs.org
Accept: */*
HTTP/1.1 302 Found
Date: Mon, 18 May 2015 19:11:21 GMT
Server Apache/2.2.22 (Ubuntu) is not blacklisted
Server: Apache/2.2.22 (Ubuntu)
Location:
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Vary: Accept-Encoding
Content-Length: 337
Content-Type: text/html; charset=iso-8859-1
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Connection #0 to host gerrit.gromacs.org left intact
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Protocol https not supported or disabled in libcurl
Closing connection -1
-- Configuring incomplete, errors occurred!
See also
/export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeOutput.log.
See also
/export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeError.log.
-
the content of CMakeOutput.log file is as follows:
The system is: Linux - 2.6.32-431.11.2.el6.x86_64 - x86_64
Compiling the C compiler identification source file CMakeCCompilerId.c
succeeded.
Compiler: /usr/bin/cc
Build flags:
Id flags:
The output was:
0
Compilation of the C compiler identification source CMakeCCompilerId.c
produced a.out
The C compiler identification is GNU, found in
/export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/3.2.2/CompilerIdC/a.out
Compiling the CXX compiler identification source file
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Compiler: /usr/bin/c++
Build flags:
Id flags:
The output was:
0
Compilation of the CXX compiler identification source
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The CXX compiler identification is GNU, found in
/export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/3.2.2/CompilerIdCXX/a.out
Determining if the C compiler works passed with the following output:
Change Dir: /export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeTmp
Run Build Command:/usr/bin/gmake cmTryCompileExec2875484959/fast
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec2875484959.dir/build.make
CMakeFiles/cmTryCompileExec2875484959.dir/build
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CMakeOutput.log 1317L, 113885C
--
the content of CMakeError.log file is as follows:
Performing C SOURCE FILE Test CFLAGS_EXCESS_PREC failed with the following
output:
Change Dir: /export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeTmp
Run Build Command:/usr/bin/gmake cmTryCompileExec2440156335/fast
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec2440156335.dir/build.make
CMakeFiles/cmTryCompileExec2440156335.dir/build
gmake[1]: Entering directory
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gmake: *** [cmTryCompileExec2440156335/fast] Error 2
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Re: [gmx-users] question
On Mon, May 18, 2015 at 9:15 PM Andrew Bostick andrew.bosti...@gmail.com wrote: Dear Mark I installed the newest version of cmake (3.2.2). After using cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON CUDA_TOOLKIT_ROOT_DIR not found or specified -- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY) (Required is at least version 4.0) -- No compatible CUDA toolkit found (v4.0+), disabling native GPU acceleration -- The GROMACS-managed build of FFTW 3 will configure with the following optimizations: --enable-sse2 Downloading: http://gerrit.gromacs.org/download/regressiontests-5.0.5.tar.gz -- [download 100% complete] CMake Error at tests/CMakeLists.txt:57 (message): error: downloading 'http://gerrit.gromacs.org/download/regressiontests-5.0.5.tar.gz' failed status_code: 1 status_string: Unsupported protocol log: Hostname was NOT found in DNS cache Trying 130.237.25.133... Connected to gerrit.gromacs.org (130.237.25.133) port 80 (#0) GET /download/regressiontests-5.0.5.tar.gz HTTP/1.1 User-Agent: curl/7.38.0 Host: gerrit.gromacs.org Accept: */* HTTP/1.1 302 Found Date: Mon, 18 May 2015 19:11:21 GMT Server Apache/2.2.22 (Ubuntu) is not blacklisted Server: Apache/2.2.22 (Ubuntu) Location: https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz Vary: Accept-Encoding Content-Length: 337 Content-Type: text/html; charset=iso-8859-1 Ignoring the response-body !DOCTYPE HTML PUBLIC -//IETF//DTD HTML 2.0//EN htmlhead title302 Found/title /headbody h1Found/h1 pThe document has moved a href= https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz here/a./p hr addressApache/2.2.22 (Ubuntu) Server at gerrit.gromacs.org Port 80/address /body/html Connection #0 to host gerrit.gromacs.org left intact Issue another request to this URL: 'https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz' Protocol https not supported or disabled in libcurl All of the above redirection is correct behaviour for our setup, but the problem is that your CMake is linking to an unsuitable version of libcurl. See http://www.cmake.org/pipermail/cmake-developers/2013-July/019430.html for background. You can maybe change your openssl library, file a bug with Ubuntu, use a Kitware-provided CMake binary, build your own, download the GROMACS tests yourself... Mark Closing connection -1 -- Configuring incomplete, errors occurred! See also /export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeOutput.log. See also /export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeError.log. - the content of CMakeOutput.log file is as follows: The system is: Linux - 2.6.32-431.11.2.el6.x86_64 - x86_64 Compiling the C compiler identification source file CMakeCCompilerId.c succeeded. Compiler: /usr/bin/cc Build flags: Id flags: The output was: 0 Compilation of the C compiler identification source CMakeCCompilerId.c produced a.out The C compiler identification is GNU, found in /export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/3.2.2/CompilerIdC/a.out Compiling the CXX compiler identification source file CMakeCXXCompilerId.cpp succeeded. Compiler: /usr/bin/c++ Build flags: Id flags: The output was: 0 Compilation of the CXX compiler identification source CMakeCXXCompilerId.cpp produced a.out The CXX compiler identification is GNU, found in /export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/3.2.2/CompilerIdCXX/a.out Determining if the C compiler works passed with the following output: Change Dir: /export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeTmp Run Build Command:/usr/bin/gmake cmTryCompileExec2875484959/fast /usr/bin/gmake -f CMakeFiles/cmTryCompileExec2875484959.dir/build.make CMakeFiles/cmTryCompileExec2875484959.dir/build @ CMakeOutput.log 1317L, 113885C -- the content of CMakeError.log file is as follows: Performing C SOURCE FILE Test CFLAGS_EXCESS_PREC failed with the following output: Change Dir: /export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeTmp Run Build Command:/usr/bin/gmake cmTryCompileExec2440156335/fast /usr/bin/gmake -f CMakeFiles/cmTryCompileExec2440156335.dir/build.make CMakeFiles/cmTryCompileExec2440156335.dir/build gmake[1]: Entering directory `/state/partition1/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeTmp' /usr/local/bin/cmake -E cmake_progress_report /export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeTmp/CMakeFiles 1 Building C object CMakeFiles/cmTryCompileExec2440156335.dir/src.c.o /usr/bin/cc -DCFLAGS_EXCESS_PREC -fexcess-precision=fast -o CMakeFiles/cmTryCompileExec2440156335.dir/src.c.o -c
Re: [gmx-users] mdp options for charmm27 force field in gromacs version 4.6.7
Dear Justin: Thank you for the suggestion. I don't use gromacs 5 because of things like this: http://redmine.gromacs.org/issues/1603 that tend to pop up early in a release series. Until I needed to run charmm simulations, I use 4.6.7 because it works and I am confident in it. But your suggestion is really good... use gmx 5 to get energies to test against gmx 4 and see if I can find valid settings. Thank you, Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: 18 May 2015 20:29 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] mdp options for charmm27 force field in gromacs version 4.6.7 On 5/18/15 2:21 PM, Christopher Neale wrote: Dear Users: I would like to use the charmm27 force field in gromacs version 4.6.7 and I would like to know if it is possible to get the proper treatment of vdw interactions. Information for gromacs 5 is here: http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM However, Gromacs 4.6.7 does not contain the option for vdw-modifier = force-switch Invalid enum 'force-switch' for variable vdw-modifier, using 'Potential-shift-Verlet' Next time use one of: 'Potential-shift-Verlet' 'Potential-shift' 'None' 'Potential-switch' 'Exact-cutoff' Is a potential-shift the same as a force-switch and therefore the following options are correct for charmm27 in gromacs 4.6.7? ns_type = grid cutoff-scheme = verlet vdwtype = cut-off rlist = 1.2 rvdw = 1.2 rvdw-switch = 1.0 rcoulomb = 1.2 vdw-modifier = Potential-shift-Verlet coulombtype = PME I know this has been discussed before on the list, but I can't find anything that seems authoritative for gromacs versions prior to v5. I cannot personally attest to anything aside from what's on the wiki. We have verified the forces are equivalent between CHARMM's vfswitch and GROMACS' force-switch modifier. This is how we do all our simulations, so for posterity, what I wrote on the wiki is what I must emphasize is known to be correct. From the manual, it seems that the group scheme + vdwtype = shift is equivalent to the modern force-switch modifier. The language of potential-shift does not sound as if it is the same as force-switch, and I don't know why such redundancy would be present anyway; perhaps legacy naming reasons. Any reason why you can't use 5.0 with the known correct settings? The check I would do is a single-point energy with the settings you think are equivalent and want to test and print out the forces with gmx traj. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
Re: [gmx-users] Gromacs in UBUNTU
Thanks Marks and really sorry for all trouble because of my stupid understanding... On 18 May 2015 at 20:58, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Use gmx_mpi solvate. You can get away with using pdb2gmx_mpi in GROMACS 5 just like old GROMACS versions only because those are magically transformed into things like gmx_mpi pdb2gmx, to provide a year of backwards compatibility. But providing backwards compatibility for a new name was not really a good thing to do, so there is no solvate_mpi. GROMACS 5.1 will remove the old-style names without gmx prefixes, so people need to start getting used to using the gmx prefix (or learn to roll their own symlinks). Mark On Mon, May 18, 2015 at 5:19 PM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: I am still not clear because pdb2gmx_mpi, editconf_mpi commands are working very well. Although they have mpi suffix but its working as non-MPI. Do I have to re-run with (DGMX_MPI=OFF -DGMX_DEFAULT_SUFFIX=OFF ) to get gmx solvate command ... Kindly explain. On 18 May 2015 at 20:39, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, These are not the installation steps you said you followed. Those previous instructions were for a non-MPI build. You've done an MPI build, which explains all your problems. Please be precise ;-) On Mon, May 18, 2015 at 3:55 PM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: definitely yes.. Then only I came to know about this gmx solvant... else How could I? I don't know. The tool is called gmx solvate. my installation steps are follwoing - -- # tar xfz gromacs-5.0.4.tar.gz # cd gromacs-5.0.4 # mkdir build # cd build #sudo CMAKE_PREFIX_PATH=/soft/fftw333/lib cmake .. -DFFTWF_INCLUDE_DIR=/soft/fftw333/include -DFFTWF_LIBRARIES=/soft/fftw333/lib/libfftw3.so -DCMAKE_INSTALL_PREFIX=/soft/gmx504 -DGMX_X11=OFF -DCMAKE_CXX_COMPILER=/usr/bin/mpicxx -DCMAKE_C_COMPILER=/usr/bin/mpicc -DGMX_MPI=ON -DGMX_DOUBLE=OFF -DGMX_DEFAULT_SUFFIX=ON -DGMX_PREFER_STATIC_LIBS=ON You have only installed an MPI build, where gmx gets suffixed to gmx_mpi. If you want the non-MPI tools (which is normal, since only mdrun works with MPI), make and install a non-MPI build. Mark # sudo make # sudo make install # sudo make install-mdrun # source /usr/local/gromacs/bin/GMXRC # ls /soft/gmx504/bin/ demux.pl g_density_mpi g_gyrate_mpi GMXRC.bash g_rms_mpi g_tune_pme_mpi do_dssp_mpi g_densmap_mpi g_h2order_mpi GMXRC.cshgrompp_mpi g_vanhove_mpi editconf_mpi g_densorder_mpi g_hbond_mpi GMXRC.zshg_rotacf_mpi g_velacc_mpi eneconv_mpi g_dielectric_mpi g_helix_mpi g_nmeig_mpi g_rotmat_mpi g_wham_mpi g_anadock_mpig_dipoles_mpi g_helixorient_mpi g_nmens_mpi g_saltbr_mpi g_wheel_mpi g_anaeig_mpi g_disre_mpi g_hydorder_mpi g_nmtraj_mpi g_sans_mpi g_x2top_mpi g_analyze_mpig_dist_mpig_lie_mpi g_options_mpig_sas_mpi make_edi_mpi g_angle_mpi g_dos_mpi g_mdmat_mpi g_order_mpi g_saxs_mpi make_ndx_mpi g_bar_mpig_dyecoupl_mpig_mindist_mpi g_pme_error_mpi g_select_mpi mdrun_mpi g_bond_mpi g_dyndom_mpi g_morph_mpi g_polystat_mpi g_sgangle_mpi mk_angndx_mpi g_bundle_mpi genbox_mpig_msd_mpi g_potential_mpi g_sham_mpi pdb2gmx_mpi g_chi_mpigenconf_mpi gmxcheck_mpi g_principal_mpi g_sigeps_mpi tpbconv_mpi g_cluster_mpig_enemat_mpi gmx-completion.bash g_protonate_mpi g_sorient_mpi trjcat_mpi g_clustsize_mpi g_energy_mpi gmx-completion-gmx_mpi.bash g_rama_mpi g_spatial_mpi trjconv_mpi g_confrms_mpigenion_mpigmxdump_mpi g_rdf_mpig_spol_mpi trjorder_mpi g_covar_mpi genrestr_mpi gmx_mpi g_rmsdist_mpig_tcaf_mpi xplor2gmx.pl g_current_mpig_filter_mpi GMXRC g_rmsf_mpi g_traj_mpi xpm2ps_mpi which doesn't have that gmx commands On 18 May 2015 at 17:40, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Did you go and read the webpage that is suggested by the rest of that message? Mark On Mon, May 18, 2015 at 12:57 PM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: sorry.. I mean pdb2gmx, editconf, genion, grompp and mdrun even it has genbox but it says This tool has been removed from Gromacs 5.0. On 18 May 2015 at 15:38, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, What other commands are working? Please be specific, we don't have time to spend on guesses :-)
[gmx-users] Gromacs Error
Dear All, i'm geting below error while subjecting my system (Protein-ligand) for equlibriation in nvt.mdp file mgmibt@mgmibt:~/gromacs-4.5.3/recent/files$ grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr :-) G R O M A C S (-: GRowing Old MAkes el Chrono Sweat :-) VERSION 4.5.3 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (-: Option Filename Type Description -f nvt.mdp Input grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c em.gro Input Structure file: gro g96 pdb tpr etc. -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -n index.ndx Input, Opt! Index file -p topol.top Input Topology file -pp processed.top Output, Opt. Topology file -o nvt.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -nice int 0 Set the nicelevel -[no]v bool no Be loud and noisy -time real -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int 0 Number of allowed warnings during input processing -[no]zero bool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Ignoring obsolete mdp entry 'title' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.18# ERROR 1 [file nvt.mdp]: With coulombtype = PME-Switch, rcoulomb must be = rlist Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'UNT' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL' turning all bonds into constraints... Setting gen_seed to 3507 Velocities were taken from a Maxwell distribution at 300 K --- Program grompp, VERSION 4.5.3 Source code file: grompp.c, line: 1356 Fatal error: There was 1 error in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Yeah, a Wuzz, Or a Jerk (F. Black) With Best Regards. Mr.Manoj Damale, M.S. Pharma (Pharmacoinformatics) NIPER, Kolkata, West Bengal State, India. -- 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] position resrtraints
On 5/18/15 8:47 AM, soumadwip ghosh wrote: Dear Justin, thanka 4 ur prompt reply. I checked that there was another issue. I didnot modify the aminoacids.rtp file in order to incorporate the new graphene.pdb atom types according to the force field. It appears to me that the correct interaction is not arsising because the atoms mentioned in the PDB file is alien to the force field. Is it the case? Should I modify the aminoacids .rtp file to None of this makes any sense to me. account for the sp2 carbon atoms and the terminal hydrogens mentioned in the PDB file and then procced without really bothering about pdb2gmx and position restraints? I think I made a very silly mistake to begin with. I really don't know how restraints factor in here. You have a suboptimal force field and an inadequate simulation time to observe the phenomenon you want. Those are your primary problems. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Protein-Ligand complex Implicit simulation
On 5/18/15 3:35 PM, sunita gupta wrote: Hello Everyone, I am trying to do protein-ligand complex simulation with implicit solvent parameters using gromacs. As, ligand parameters are not present in gbsa.itp, I added all the possible atomtypes and their van der wall radii from gaff ff and also managed to get get the HCT paremeters. Still its giving errorsAnyone please suggest me how to proceed further. Without knowing what errors you're getting, the only answer is you're still doing something wrong. Ask a generic question, get a generic answer :) -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] mdp options for charmm27 force field in gromacs version 4.6.7
On 5/18/15 2:21 PM, Christopher Neale wrote: Dear Users: I would like to use the charmm27 force field in gromacs version 4.6.7 and I would like to know if it is possible to get the proper treatment of vdw interactions. Information for gromacs 5 is here: http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM However, Gromacs 4.6.7 does not contain the option for vdw-modifier = force-switch Invalid enum 'force-switch' for variable vdw-modifier, using 'Potential-shift-Verlet' Next time use one of: 'Potential-shift-Verlet' 'Potential-shift' 'None' 'Potential-switch' 'Exact-cutoff' Is a potential-shift the same as a force-switch and therefore the following options are correct for charmm27 in gromacs 4.6.7? ns_type = grid cutoff-scheme = verlet vdwtype = cut-off rlist = 1.2 rvdw = 1.2 rvdw-switch = 1.0 rcoulomb = 1.2 vdw-modifier = Potential-shift-Verlet coulombtype = PME I know this has been discussed before on the list, but I can't find anything that seems authoritative for gromacs versions prior to v5. I cannot personally attest to anything aside from what's on the wiki. We have verified the forces are equivalent between CHARMM's vfswitch and GROMACS' force-switch modifier. This is how we do all our simulations, so for posterity, what I wrote on the wiki is what I must emphasize is known to be correct. From the manual, it seems that the group scheme + vdwtype = shift is equivalent to the modern force-switch modifier. The language of potential-shift does not sound as if it is the same as force-switch, and I don't know why such redundancy would be present anyway; perhaps legacy naming reasons. Any reason why you can't use 5.0 with the known correct settings? The check I would do is a single-point energy with the settings you think are equivalent and want to test and print out the forces with gmx traj. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] RDF
Hi Justin The fact is I want to calculate water density in the system. If I select group1: oxygen and group2: oxygen, g_rdf command gives me very large numbers. Is it the number of atoms that should be changed to g/cm3? Besides, what does it calculate, each O is a reference atom during calculation? Thanks a lot! On Sun, May 17, 2015 at 2:17 PM, mah maz mahma...@gmail.com wrote: Dear all, I want to calculate the radial distribution function of water molecules in my system. I use g_rdf -f traj.xtc -n -o. It gives me large numbers which is not logical I suppose. Is it meaningful if I separate oxygen and hydrogen atoms in the index file and calculate the RDF for O-O atoms? Is reference atom necessary to get RDF? Thanks! -- 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] Force field parameterization for PAMAM dendrimers
Dear all, I want to perform MD simuations on PAMAM dendrimers, but unfortunately this molecule has not been defined in any of the GROMACS force fields. Therefore, I should parameterize the force field for my purpose. How should I do this procedure? (It is mentionable that I read the http://www.gromacs.org/Documentation/How-tos/Parameterization but I could not perform any runs!) Truly yours, Farideh -- 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] increasing simulation time via temperature rising
Hi all I'm studying effect of temperature on incredibly stable protein. I've started simulating at 300K then, 400K and 500K. 30ns simulating takes about 4days for these three temperature in a same system. when I want to run 30ns simulation at 600K, it will take more than 20 days does rising temperature, have any affect on time of simulation? is this increasing in time reasonable? thanks -- 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] increasing simulation time via temperature rising
Hi Nazli, No, that's not related to temperature. Otherwise you'd probably see a trend. I guess with the 600K simulation you have another process that interferes and eats CPU. Mind that a simulation running on four/eight cores will be affected significantly by anything that uses a considerable part of a CPU. Cheers, Tsjerk On May 18, 2015 08:48, nazli kashani javid nazlikja...@gmail.com wrote: Hi all I'm studying effect of temperature on incredibly stable protein. I've started simulating at 300K then, 400K and 500K. 30ns simulating takes about 4days for these three temperature in a same system. when I want to run 30ns simulation at 600K, it will take more than 20 days does rising temperature, have any affect on time of simulation? is this increasing in time reasonable? thanks -- 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.
Re: [gmx-users] question
Hi, I think you just hit a moment when the server was not available. Please try again. Mark On Sun, 17 May 2015 16:44 Andrew Bostick andrew.bosti...@gmail.com wrote: Dear Justin Thanks for your answer. At first, I installed cmake 2.8.8 on centOS, by following commands: ./bootstrap; gmake; make install Then I used *Quick and dirty *installation http://www.gromacs.org/Documentation/Installation_Instructions_5.0?highlight=installation#TOC instruction. When I used cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON I encountered with: [root@lbm build]# cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON CUDA_TOOLKIT_ROOT_DIR not found or specified -- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY) (Required is at least version 4.0) -- No compatible CUDA toolkit found (v4.0+), disabling native GPU acceleration -- The GROMACS-managed build of FFTW 3 will configure with the following optimizations: --enable-sse2 Downloading: http://gerrit.gromacs.org/download/regressiontests-5.0.5.tar.gz -- [download 100% complete] CMake Error at tests/CMakeLists.txt:57 (message): error: downloading ' http://gerrit.gromacs.org/download/regressiontests-5.0.5.tar.gz' failed status_code: 1 status_string: unsupported protocol log: About to connect() to gerrit.gromacs.org port 80 (#0) Trying 130.237.25.133... connected Connected to gerrit.gromacs.org (130.237.25.133) port 80 (#0) GET /download/regressiontests-5.0.5.tar.gz HTTP/1.1 Host: gerrit.gromacs.org Accept: */* HTTP/1.1 302 Found Date: Sun, 17 May 2015 14:37:01 GMT Server: Apache/2.2.22 (Ubuntu) Location: https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz Vary: Accept-Encoding Content-Length: 337 Content-Type: text/html; charset=iso-8859-1 Ignoring the response-body !DOCTYPE HTML PUBLIC -//IETF//DTD HTML 2.0//EN htmlhead title302 Found/title /headbody h1Found/h1 pThe document has moved a href= https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz here/a./p hr addressApache/2.2.22 (Ubuntu) Server at gerrit.gromacs.org Port 80/address /body/html Connection #0 to host gerrit.gromacs.org left intact Issue another request to this URL: ' https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz' libcurl was built with SSL disabled, https: not supported! unsupported protocol Closing connection #0 -- Configuring incomplete, errors occurred! == What is wrong in my installation steps? Thanks in advance. -- 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.
Re: [gmx-users] energy minimization problem
Hi Tsjerk, My computer has 8 cores only, martini simulation looks much faster than full atomic simulation. The command I used is here: python martinize.py -f hyp.pdb -o system-vaccum.top -x hyp-CG.pdb -ss hyp_lys -p backbone -ff martini22 -collagen editconf -f hyp-CG.pdb -c -d 1 -o hyp-CG-box.pdb grompp -f minimization-vaccum.mdp -p system-vaccum.top -c hyp-CG-box.pdb -o minimization-vaccum.tpr mdrun -deffnm minimization-vaccum -v gmx solvate -cp minimization-vaccum.gro -cs water-box-CG_303K-1bar.gro -radius 0.21 -o system-solvated.gro I downloaded the CG water model from martini protein tutorial website. Is there anything wrong? -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Monday, 18 May 2015 6:47 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] energy minimization problem Hi Ming Tang, That's pretty quick. I guess that this is on multiple cores, given the size of the system. It often helps to equilibrate on a limited number of cores, but I'm not sure that's feasible. Did you obtain the model by martinizing the original structure, or did you use the relaxed structure from the atomistic simulation? How did you solvate the system? Cheers, Tsjerk On May 18, 2015 10:29, Ming Tang m21.t...@qut.edu.au wrote: Hi Tsjerk, I just tried, but it stopped for too many LICS warnings at step 6000. Small triple helix can be equilibrated for 1000ns with NPT. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Monday, 18 May 2015 6:21 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] energy minimization problem Hi Ming Tang, Can you run in NVT? Then afterwards you can try NPT without position restraints. Cheers, Tsjerk On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote: Thanks a lot, Justin It really makes me feel weird. The small triple helix with 30 amino acids per chain(generated simply by deleting other atoms in .pdb file of the real triple helix) can be equilibrated for 1ns using exactly the same control files, and the real triple helix can be used for full atomic simulation without any problem. The CG topology is generated using the same mitinize.py downloaded from the website. I will try for another time, and will tell you if I fix it. Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Sunday, 17 May 2015 7:07 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/16/15 8:30 AM, Ming Tang wrote: Dear Justin, I tried to use small time step. First, set dt=0.005ps, after running 20ps, I found one chain of the triple helix just went to another water box totally. I guess there is something wrong with the martini ff because of the small time step. Then, I increased it to 0.01ps, after running 40ps, I checked the .gro, and found all the three chains stay together, which is reasonable. However, even use dt=0.01, the simulation can only run about 1ns. And, after simulating 100 ps using dt=0.01ps, the simulation can just run thousands of steps when dt is increased to 0.02ps. I tried many times and many different time steps, but still could not see the possibility for it to run hundreds of nanoseconds, which is quite normal when using martini force. If the system can be further minimized, then it can run longer maybe. This seems entirely random and suggests instead that there is something simply physically unstable with the system or problematic in the topology. I don't use MARTINI (or CG models in general) so there's little else I can suggest. Maybe someone more experienced with such systems will chime in. Also note that a chain moving into another box is probably just a PBC effect and not a true dissociation. If it is a dissociation, it's not simply because of the time step. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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
Re: [gmx-users] energy minimization problem
Hi Tsjerk, I used the original structure generated by sabbac. My computer has 8 cores only, martini simulation looks much faster than full atomic simulation. The command I used is here: python martinize.py -f hyp.pdb -o system-vaccum.top -x hyp-CG.pdb -ss hyp_lys -p backbone -ff martini22 -collagen editconf -f hyp-CG.pdb -c -d 1 -o hyp-CG-box.pdb grompp -f minimization-vaccum.mdp -p system-vaccum.top -c hyp-CG-box.pdb -o minimization-vaccum.tpr mdrun -deffnm minimization-vaccum -v gmx solvate -cp minimization-vaccum.gro -cs water-box-CG_303K-1bar.gro -radius 0.21 -o system-solvated.gro I downloaded the CG water model from martini protein tutorial website. Is there anything wrong? -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Monday, 18 May 2015 6:47 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] energy minimization problem Hi Ming Tang, That's pretty quick. I guess that this is on multiple cores, given the size of the system. It often helps to equilibrate on a limited number of cores, but I'm not sure that's feasible. Did you obtain the model by martinizing the original structure, or did you use the relaxed structure from the atomistic simulation? How did you solvate the system? Cheers, Tsjerk On May 18, 2015 10:29, Ming Tang m21.t...@qut.edu.au wrote: Hi Tsjerk, I just tried, but it stopped for too many LICS warnings at step 6000. Small triple helix can be equilibrated for 1000ns with NPT. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Monday, 18 May 2015 6:21 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] energy minimization problem Hi Ming Tang, Can you run in NVT? Then afterwards you can try NPT without position restraints. Cheers, Tsjerk On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote: Thanks a lot, Justin It really makes me feel weird. The small triple helix with 30 amino acids per chain(generated simply by deleting other atoms in .pdb file of the real triple helix) can be equilibrated for 1ns using exactly the same control files, and the real triple helix can be used for full atomic simulation without any problem. The CG topology is generated using the same mitinize.py downloaded from the website. I will try for another time, and will tell you if I fix it. Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Sunday, 17 May 2015 7:07 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/16/15 8:30 AM, Ming Tang wrote: Dear Justin, I tried to use small time step. First, set dt=0.005ps, after running 20ps, I found one chain of the triple helix just went to another water box totally. I guess there is something wrong with the martini ff because of the small time step. Then, I increased it to 0.01ps, after running 40ps, I checked the .gro, and found all the three chains stay together, which is reasonable. However, even use dt=0.01, the simulation can only run about 1ns. And, after simulating 100 ps using dt=0.01ps, the simulation can just run thousands of steps when dt is increased to 0.02ps. I tried many times and many different time steps, but still could not see the possibility for it to run hundreds of nanoseconds, which is quite normal when using martini force. If the system can be further minimized, then it can run longer maybe. This seems entirely random and suggests instead that there is something simply physically unstable with the system or problematic in the topology. I don't use MARTINI (or CG models in general) so there's little else I can suggest. Maybe someone more experienced with such systems will chime in. Also note that a chain moving into another box is probably just a PBC effect and not a true dissociation. If it is a dissociation, it's not simply because of the time step. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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
Re: [gmx-users] Force field parameterization for PAMAM dendrimers
Dear Farideh, We have recently published an article on PAMAM dendrimers. We used oplsaa forcefield. You can access the paper at http://pubs.rsc.org/en/content/articlelanding/2015/sm/c5sm00854a. Hope it helps. Chandan On Mon, May 18, 2015 at 12:58 PM, faride badalkhani farideh.kham...@gmail.com wrote: Dear all, I want to perform MD simuations on PAMAM dendrimers, but unfortunately this molecule has not been defined in any of the GROMACS force fields. Therefore, I should parameterize the force field for my purpose. How should I do this procedure? (It is mentionable that I read the http://www.gromacs.org/Documentation/How-tos/Parameterization but I could not perform any runs!) Truly yours, Farideh -- 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. -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India *All work and no play makes Jack a dull boy...”* -- 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] energy minimization problem
Besides, the martini.itp does not contain moleculetype CL, so I edit it like this: [ moleculetype ] ; molname nrexcl CL1 [ atoms ] ;id typeresnr residu atomcgnrcharge 1 P4 1 CL CL 1 -1 Please help to have a look. I do not know whether it is true or not, as the small triple helix used for test does not carry charge, so I did not add CL. Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Ming Tang Sent: Monday, 18 May 2015 7:04 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem Hi Tsjerk, I used the original structure generated by sabbac. My computer has 8 cores only, martini simulation looks much faster than full atomic simulation. The command I used is here: python martinize.py -f hyp.pdb -o system-vaccum.top -x hyp-CG.pdb -ss hyp_lys -p backbone -ff martini22 -collagen editconf -f hyp-CG.pdb -c -d 1 -o hyp-CG-box.pdb grompp -f minimization-vaccum.mdp -p system-vaccum.top -c hyp-CG-box.pdb -o minimization-vaccum.tpr mdrun -deffnm minimization-vaccum -v gmx solvate -cp minimization-vaccum.gro -cs water-box-CG_303K-1bar.gro -radius 0.21 -o system-solvated.gro I downloaded the CG water model from martini protein tutorial website. Is there anything wrong? -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Monday, 18 May 2015 6:47 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] energy minimization problem Hi Ming Tang, That's pretty quick. I guess that this is on multiple cores, given the size of the system. It often helps to equilibrate on a limited number of cores, but I'm not sure that's feasible. Did you obtain the model by martinizing the original structure, or did you use the relaxed structure from the atomistic simulation? How did you solvate the system? Cheers, Tsjerk On May 18, 2015 10:29, Ming Tang m21.t...@qut.edu.au wrote: Hi Tsjerk, I just tried, but it stopped for too many LICS warnings at step 6000. Small triple helix can be equilibrated for 1000ns with NPT. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Monday, 18 May 2015 6:21 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] energy minimization problem Hi Ming Tang, Can you run in NVT? Then afterwards you can try NPT without position restraints. Cheers, Tsjerk On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote: Thanks a lot, Justin It really makes me feel weird. The small triple helix with 30 amino acids per chain(generated simply by deleting other atoms in .pdb file of the real triple helix) can be equilibrated for 1ns using exactly the same control files, and the real triple helix can be used for full atomic simulation without any problem. The CG topology is generated using the same mitinize.py downloaded from the website. I will try for another time, and will tell you if I fix it. Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Sunday, 17 May 2015 7:07 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/16/15 8:30 AM, Ming Tang wrote: Dear Justin, I tried to use small time step. First, set dt=0.005ps, after running 20ps, I found one chain of the triple helix just went to another water box totally. I guess there is something wrong with the martini ff because of the small time step. Then, I increased it to 0.01ps, after running 40ps, I checked the .gro, and found all the three chains stay together, which is reasonable. However, even use dt=0.01, the simulation can only run about 1ns. And, after simulating 100 ps using dt=0.01ps, the simulation can just run thousands of steps when dt is increased to 0.02ps. I tried many times and many different time steps, but still could not see the possibility for it to run hundreds of nanoseconds, which is quite normal when using martini force. If the system can be further minimized, then it can run longer maybe. This seems entirely random and suggests instead that there is something simply physically unstable with the system or problematic in the topology. I don't use MARTINI (or CG models in general) so there's little else I can suggest. Maybe someone more experienced with such systems will chime in. Also note that a chain moving into another box is probably just a PBC effect and not a true dissociation. If it is a
Re: [gmx-users] increasing simulation time via temperature rising
Hi Nazli, Also, I doubt simulations beyond 400 K make any sense: not only such conditions are implausible for a protein to exist in, but, as far as I know, the force fields are not parametrized to work so far beyond room temperature. cheers, M. 2015-05-18 9:05 GMT+02:00 Tsjerk Wassenaar tsje...@gmail.com: Hi Nazli, No, that's not related to temperature. Otherwise you'd probably see a trend. I guess with the 600K simulation you have another process that interferes and eats CPU. Mind that a simulation running on four/eight cores will be affected significantly by anything that uses a considerable part of a CPU. Cheers, Tsjerk On May 18, 2015 08:48, nazli kashani javid nazlikja...@gmail.com wrote: Hi all I'm studying effect of temperature on incredibly stable protein. I've started simulating at 300K then, 400K and 500K. 30ns simulating takes about 4days for these three temperature in a same system. when I want to run 30ns simulation at 600K, it will take more than 20 days does rising temperature, have any affect on time of simulation? is this increasing in time reasonable? thanks -- 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. -- 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] energy minimization problem
Hi Tsjerk, This protein has a total charge of 35e, and I added 35 CL to balance the system. Is there any difference between adding CL and not adding CL? Thank you. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Monday, 18 May 2015 6:21 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] energy minimization problem Hi Ming Tang, Can you run in NVT? Then afterwards you can try NPT without position restraints. Cheers, Tsjerk On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote: Thanks a lot, Justin It really makes me feel weird. The small triple helix with 30 amino acids per chain(generated simply by deleting other atoms in .pdb file of the real triple helix) can be equilibrated for 1ns using exactly the same control files, and the real triple helix can be used for full atomic simulation without any problem. The CG topology is generated using the same mitinize.py downloaded from the website. I will try for another time, and will tell you if I fix it. Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Sunday, 17 May 2015 7:07 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/16/15 8:30 AM, Ming Tang wrote: Dear Justin, I tried to use small time step. First, set dt=0.005ps, after running 20ps, I found one chain of the triple helix just went to another water box totally. I guess there is something wrong with the martini ff because of the small time step. Then, I increased it to 0.01ps, after running 40ps, I checked the .gro, and found all the three chains stay together, which is reasonable. However, even use dt=0.01, the simulation can only run about 1ns. And, after simulating 100 ps using dt=0.01ps, the simulation can just run thousands of steps when dt is increased to 0.02ps. I tried many times and many different time steps, but still could not see the possibility for it to run hundreds of nanoseconds, which is quite normal when using martini force. If the system can be further minimized, then it can run longer maybe. This seems entirely random and suggests instead that there is something simply physically unstable with the system or problematic in the topology. I don't use MARTINI (or CG models in general) so there's little else I can suggest. Maybe someone more experienced with such systems will chime in. Also note that a chain moving into another box is probably just a PBC effect and not a true dissociation. If it is a dissociation, it's not simply because of the time step. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- 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.
Re: [gmx-users] Gromacs in UBUNTU
Hi actually all other commands are working fine. only when I am runing: -- g@chandan:~$ gmx solvate -cp protein.pdb -cs tip4p.gro -p topol.top -o solv.pdb No command 'gmx' found, did you mean: Command 'gm' from package 'graphicsmagick' (universe) Command 'gcx' from package 'gcx' (universe) Command 'gmt' from package 'libgenome-perl' (universe) Command 'ngmx' from package 'gromacs' (universe) gmx: command not found --- this error is coming. gmx solvant doesn't exist, of course, but I assume that was a typo! I have all options but its not working and even it doesn't show like other commands in the installation dir /soft/gmx504/bin/ what else to try!! On 18 May 2015 at 13:11, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, You may need to give your normal user account read permission to that directory. gmx solvant doesn't exist, of course, but I assume that was a typo! :-) Mark On Mon, May 18, 2015 at 6:58 AM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: Dear all I followed the same steps to install Gromacs - 5.0.4 in ubuntu - 14.04 (64bit) and seems like things get installed but I am not able to get gmx solvant command. I have searched in my installation dir /soft/gmx504/bin/ and also source /soft/gmx504/bin/GMXRC.bash in my bashrc file. Kindly help. with regards Sanchaita On 14 May 2015 at 08:54, James Lord jjamesgreen...@gmail.com wrote: Hi Saeed, You don't necessarily need to install it first from Ubuntu software center and then update it. you can directly get the latest version and follow the instruction on gromacs website. Quick and dirty installation http://www.gromacs.org/Documentation/Installation_Instructions_5.0?highlight=command#TOC 1. Get the latest version of your C and C++ compilers. 2. Check that you have CMake version 2.8.8 or later. 3. Get and unpack the latest version of the GROMACS tarball. 4. Make a separate build directory and change to it. 5. Run cmake with the path to the source as an argument 6. Run make, make check, and make install Or, as a sequence of commands to execute: tar xfz gromacs-5.0.5.tar.gz cd gromacs-5.0.5 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON make make check sudo make install source /usr/local/gromacs/bin/GMXRC Cheers James On Thu, May 14, 2015 at 1:53 PM, saeed poorasad s_poora...@yahoo.com wrote: Dear Gromacs users , Greetings .I want to install Gromacs with using of UBUNTU software center . Now I want to know about updating process of this version of gromacs . Does it update automatically with Ubuntu ? Thanks for your attention .Best,Saeed. -- 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. -- 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. -- 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] Gromacs in UBUNTU
Hi, What other commands are working? Please be specific, we don't have time to spend on guesses :-) Mark On Mon, 18 May 2015 11:06 Sanchaita Rajkhowa srajkhow...@gmail.com wrote: Hi actually all other commands are working fine. only when I am runing: -- g@chandan:~$ gmx solvate -cp protein.pdb -cs tip4p.gro -p topol.top -o solv.pdb No command 'gmx' found, did you mean: Command 'gm' from package 'graphicsmagick' (universe) Command 'gcx' from package 'gcx' (universe) Command 'gmt' from package 'libgenome-perl' (universe) Command 'ngmx' from package 'gromacs' (universe) gmx: command not found --- this error is coming. gmx solvant doesn't exist, of course, but I assume that was a typo! I have all options but its not working and even it doesn't show like other commands in the installation dir /soft/gmx504/bin/ what else to try!! On 18 May 2015 at 13:11, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, You may need to give your normal user account read permission to that directory. gmx solvant doesn't exist, of course, but I assume that was a typo! :-) Mark On Mon, May 18, 2015 at 6:58 AM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: Dear all I followed the same steps to install Gromacs - 5.0.4 in ubuntu - 14.04 (64bit) and seems like things get installed but I am not able to get gmx solvant command. I have searched in my installation dir /soft/gmx504/bin/ and also source /soft/gmx504/bin/GMXRC.bash in my bashrc file. Kindly help. with regards Sanchaita On 14 May 2015 at 08:54, James Lord jjamesgreen...@gmail.com wrote: Hi Saeed, You don't necessarily need to install it first from Ubuntu software center and then update it. you can directly get the latest version and follow the instruction on gromacs website. Quick and dirty installation http://www.gromacs.org/Documentation/Installation_Instructions_5.0?highlight=command#TOC 1. Get the latest version of your C and C++ compilers. 2. Check that you have CMake version 2.8.8 or later. 3. Get and unpack the latest version of the GROMACS tarball. 4. Make a separate build directory and change to it. 5. Run cmake with the path to the source as an argument 6. Run make, make check, and make install Or, as a sequence of commands to execute: tar xfz gromacs-5.0.5.tar.gz cd gromacs-5.0.5 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON make make check sudo make install source /usr/local/gromacs/bin/GMXRC Cheers James On Thu, May 14, 2015 at 1:53 PM, saeed poorasad s_poora...@yahoo.com wrote: Dear Gromacs users , Greetings .I want to install Gromacs with using of UBUNTU software center . Now I want to know about updating process of this version of gromacs . Does it update automatically with Ubuntu ? Thanks for your attention .Best,Saeed. -- 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. -- 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. -- 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
Re: [gmx-users] Gromacs in UBUNTU
sorry.. I mean pdb2gmx, editconf, genion, grompp and mdrun even it has genbox but it says This tool has been removed from Gromacs 5.0. On 18 May 2015 at 15:38, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, What other commands are working? Please be specific, we don't have time to spend on guesses :-) Mark On Mon, 18 May 2015 11:06 Sanchaita Rajkhowa srajkhow...@gmail.com wrote: Hi actually all other commands are working fine. only when I am runing: -- g@chandan:~$ gmx solvate -cp protein.pdb -cs tip4p.gro -p topol.top -o solv.pdb No command 'gmx' found, did you mean: Command 'gm' from package 'graphicsmagick' (universe) Command 'gcx' from package 'gcx' (universe) Command 'gmt' from package 'libgenome-perl' (universe) Command 'ngmx' from package 'gromacs' (universe) gmx: command not found --- this error is coming. gmx solvant doesn't exist, of course, but I assume that was a typo! I have all options but its not working and even it doesn't show like other commands in the installation dir /soft/gmx504/bin/ what else to try!! On 18 May 2015 at 13:11, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, You may need to give your normal user account read permission to that directory. gmx solvant doesn't exist, of course, but I assume that was a typo! :-) Mark On Mon, May 18, 2015 at 6:58 AM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: Dear all I followed the same steps to install Gromacs - 5.0.4 in ubuntu - 14.04 (64bit) and seems like things get installed but I am not able to get gmx solvant command. I have searched in my installation dir /soft/gmx504/bin/ and also source /soft/gmx504/bin/GMXRC.bash in my bashrc file. Kindly help. with regards Sanchaita On 14 May 2015 at 08:54, James Lord jjamesgreen...@gmail.com wrote: Hi Saeed, You don't necessarily need to install it first from Ubuntu software center and then update it. you can directly get the latest version and follow the instruction on gromacs website. Quick and dirty installation http://www.gromacs.org/Documentation/Installation_Instructions_5.0?highlight=command#TOC 1. Get the latest version of your C and C++ compilers. 2. Check that you have CMake version 2.8.8 or later. 3. Get and unpack the latest version of the GROMACS tarball. 4. Make a separate build directory and change to it. 5. Run cmake with the path to the source as an argument 6. Run make, make check, and make install Or, as a sequence of commands to execute: tar xfz gromacs-5.0.5.tar.gz cd gromacs-5.0.5 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON make make check sudo make install source /usr/local/gromacs/bin/GMXRC Cheers James On Thu, May 14, 2015 at 1:53 PM, saeed poorasad s_poora...@yahoo.com wrote: Dear Gromacs users , Greetings .I want to install Gromacs with using of UBUNTU software center . Now I want to know about updating process of this version of gromacs . Does it update automatically with Ubuntu ? Thanks for your attention .Best,Saeed. -- 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. -- 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
[gmx-users] position rstraints
Hi all, I am trying to see the unzipping of double stranded DNA on the surface of graphene nanosheets. I am using GROMOS 53a5 force field and I obtained a graphene sheet from ATB software. i obtained both the .itp as well as the PDB from that site. Now, I proceeded for molecular dynamics withou doing pdb2gmx and without any posre file for the graphene. The dsDNA and the graphene coordinates were concatenated and throughout the euilibration and mdrun it dint give any trouble. However, after 30 ns of the mdrun, I am observing no unzipping of the DNA chain and the no.of H-bond between the parallel strands remain unchanged. Is it happening because I dint do the pdb2gmx of the graphene separately so the accurate atomic level interaction is not following? Does the non-incorporation of the posre_graphene file in the dynamics has anuthing to do with it? Should I restart after doing pdb2gmx of the graphene , obtaining the posre_graphene file and include it in the graphene.itp file provided by the ATB server? Your help is required. Hope I am not asking for much. Regards, Soumadwip Research Fellow, IIT Bombay, India -- 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] first residue in chains warning issue
Dear Justin, After minimization, I got the following note when using NPT. NOTE 1 [file topol.top, line 49]: The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has an estimated oscillational period of 1.0e-02 ps, which is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change the constraints mdp option. Does this has something to do with the warning given by pdb2gmx? When reducing dt from 0.001ps to 0.0009ps, the note is gone. Is there anything wrong with my topol.top? Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Tuesday, 12 May 2015 10:19 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] first residue in chains warning issue On 5/12/15 8:10 AM, Ming Tang wrote: Thanks Justin, At first, I wanted to choose NONE in for both N and C terminus, but it gave me the same warnings for both the first and the last residue in every chains. However, choose NH3+/COO- and NH2/COOH just gave that warning for the first residue. Right, because choosing None is chemical nonsense in this context. The angles and bonds in .itp are like this: [ bonds ] ; aiaj functc0c1c2c3 1 2 2gb_2 1 3 2gb_2 1 4 2gb_21 4 5 2gb_27 [ angles ] ; aiajak functc0c1c2 c3 2 1 3 2ga_10 2 1 4 2ga_10 2 1 5 2ga_11 3 1 4 2ga_10 3 1 5 2ga_11 4 1 5 2ga_11 1 5 6 2ga_13 1 513 2ga_13 6 513 2ga_13 Just now, I tried to delete one H atom of the first residue in the input .pdb, but got the same warnings for them. Is there anything wrong with the angle and bond? Well, cross-reference what the atoms are and what the parameters should be. That's your job, not mine :) Energy minimization and a quick MD run will show you if there are any problems; if things are missing or wrong (very unlikely, but always check when you see warnings!) then the structure will be obviously wrong very quickly. Like I said, this is really most likely just some weird case in the code that isn't handled elegantly, but there's not enough to go on for a full debug. -Justin -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Tuesday, 12 May 2015 9:35 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] first residue in chains warning issue On 5/11/15 6:48 PM, Ming Tang wrote: Hi Justin, Here is the output of pdb2gmx: Command line: pdb2gmx -f hyp_lys.pdb -o complex.gro -ignh -ter -ff gromos54a7 -water SPC Using the Gromos54a7 force field in directory gromos54a7.ff Opening force field file /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.r2b Reading hyp_lys.pdb... Read 20130 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 3 chains and 0 blocks of water and 3134 residues with 20130 atoms chain #res #atoms 1 'A' 1054 6788 2 'B' 1026 6554 3 'C' 1054 6788 All occupancies are one Opening force field file /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/atomtypes.atp Atomtype 58 Reading residue database... (gromos54a7) Opening force field file /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Residue 108 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.2# Processing chain 1 'A' (6788 atoms, 1054 residues) Analysing hydrogen-bonding network for automated assignment of histidine protonation. 1365 donors and 1444 acceptors were found. There are 1748 hydrogen bonds Will use HISE for residue 105 Will use HISE for residue 948 Identified residue GLN1 as a starting terminus. Identified residue TYR1054 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: MET2 MET19 MET55 MET102 HIS105 MET139 MET418 SD15 SD136 SD369 SD678 NE2702 SD926 SD2692 MET19
Re: [gmx-users] RDF
On 5/18/15 2:55 AM, mah maz wrote: Hi Justin The fact is I want to calculate water density in the system. If I select group1: oxygen and group2: oxygen, g_rdf command gives me very large numbers. Is it the number of atoms that should be changed to g/cm3? Besides, what does it calculate, each O is a reference atom during calculation? All of this is in the manual. The value of the RDF is the relative probability of finding a given particle as a function of distance. If you just want density, there's a separate tool for that, conveniently called g_density. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] first residue in chains warning issue
On 5/18/15 7:39 AM, Ming Tang wrote: Dear Justin, After minimization, I got the following note when using NPT. NOTE 1 [file topol.top, line 49]: The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has an estimated oscillational period of 1.0e-02 ps, which is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change the constraints mdp option. Does this has something to do with the warning given by pdb2gmx? When reducing dt from 0.001ps to 0.0009ps, the note is gone. Is there anything wrong with my topol.top? No, as the note says, you probably aren't using constraints, which if you want a 1-fs or larger value of dt, you need to be using. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] position rstraints
On 5/18/15 6:55 AM, soumadwip ghosh wrote: Hi all, I am trying to see the unzipping of double stranded DNA on the surface of graphene nanosheets. I am using GROMOS 53a5 force field and I obtained a graphene sheet from ATB software. i obtained both the .itp as well as the PDB from that site. Now, I proceeded for molecular dynamics withou doing pdb2gmx and without any posre file for the graphene. The dsDNA and the graphene coordinates were concatenated and throughout the euilibration and mdrun it dint give any trouble. However, after 30 ns of the mdrun, I am observing no unzipping of the DNA chain and the no.of H-bond between the parallel strands remain unchanged. Is it happening 30 ns is a very short amount of time. because I dint do the pdb2gmx of the graphene separately so the accurate atomic level interaction is not following? Does the non-incorporation of No, that's not a problem at all. There is no requirement to use pdb2gmx at all. the posre_graphene file in the dynamics has anuthing to do with it? Should I restart after doing pdb2gmx of the graphene , obtaining the posre_graphene file and include it in the graphene.itp file provided by the ATB server? There are two possible issues: (1) your simulation is too short and/or (2) the force field is not a good one. I don't know of any papers that have used 53A5 (which is designed for hydrophobic solvents) for DNA; recent version of CHARMM and AMBER are much better force fields for nucleic acid simulations. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
