Re: [gmx-users] Hydrogen bond breaking process
Is there any publication regarding this Fe-CO covalent bond breaking ? Actually in experimental techniques, the bond between Fe-CO in myoglobin gets broken in100 ps time scale. Is't possible to do this process by QM/MM methods or ReaxFF? Please need an advice. I haven't have any prior knowledge on this, Thanks in advance. On Mon, Sep 3, 2012 at 2:51 PM, Peter C. Lai p...@uab.edu wrote: Well there is always ReaxFF. You'd still have to use QM/MM to parameterize the various states though. On 2012-09-02 09:48:25PM -0400, Justin Lemkul wrote: On 9/2/12 9:42 PM, Rajiv Gandhi wrote: Could you tell me how can i perform for coordinate covalent bond breaking and forming between Fe-CO in myoglobin. I guess, it has been already done by some groups. If possible can you send me journals related to this. You can't break and form bonds in classical MD. That's an exercise for QM/MM. There are plenty of articles out there, a Google search would turn up hundreds, maybe even some directly related to what you want to do. -Justin Thanks. On Mon, Sep 3, 2012 at 8:55 AM, Justin Lemkul jalem...@vt.edu wrote: On 8/31/12 10:43 PM, Rajiv Gandhi wrote: Can you tell me how to predict the Hydrogen bond breaking process (For example Fe-CO hydrogen bond broken in Myoglobin at 100 ps) through MD simulation? There is no hydrogen bonding in a Fe-CO interaction. That is a coordinate covalent bond. If you want to study hydrogen bonds breaking and forming in protein structures, the pull code may be useful. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Kind regards Rajiv -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_mindist - reg
hi all, I would like to measure the hydrophobic interaction of the ligand against the protein during the simulation . From the forum I learnt g_mindist will be the better tool. But when i used the command g_mindist -f traj.xtc -s topol.tpr -n index.ndx -on numcont.xvg -group and selected protein as group1 and ligand as group 2 i get the result like this g_mindist -f traj.xtc -s pull.tpr -n index.ndx -on numcont.xvg -group # # g_mindist is part of G R O M A C S: # # Good ROcking Metal Altar for Chronical Sinners # @title Number of Contacts 0.6 nm @xaxis label Time (ps) @yaxis label Number @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend Protein-UNK 0.00e+0021 1.00e+0021 2.00e+0021 3.00e+0021 4.00e+0021 5.00e+0021 6.00e+0021 7.00e+0021 8.00e+0021 9.00e+0021 1.00e+0121 1.10e+0121 1.20e+0121 1.30e+0121 1.40e+0121 1.50e+0121 1.60e+0121 1.70e+0121 1.80e+0121 1.90e+0121 2.00e+0121 2.10e+0121 2.20e+0121 2.30e+0121 2.40e+0121 2.50e+0121 2.60e+0121 2.70e+0121 2.80e+0121 2.90e+0121 3.00e+0121 3.10e+0121 3.20e+0121 3.30e+0121 3.40e+0121 3.50e+0121 3.60e+0121 3.70e+0121 3.80e+0121 3.90e+0121 4.00e+0121 4.10e+0121 4.20e+0121 4.30e+0121 4.40e+0121 4.50e+0121 4.60e+0121 4.70e+0121 4.80e+0121 4.90e+0121 5.00e+0121 5.10e+0121 5.20e+0121 5.30e+0121 I would like to know what ever the data I've obtained is the number of hydrophobic interaction between the ligand and protein or I am wrong somewhere. Please help me. Thanks in advance -- View this message in context: http://gromacs.5086.n6.nabble.com/g-mindist-reg-tp5000756.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] au virtual atom
Thanks for your response, but I've read the manual. What I realized is that, for example, I should consider for every two, three or … atoms, a virtual atom. Here are some questions: 1 - Does not important consider which atoms together? or How much is the angle between atoms? 2 -Does I need to manually sort atoms and consider for every group a virtual site? thanks ramezani Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Adding phosphate to protein
Hi everybody, I want to add a phosphate to my protein. Is this possible with gromacs? Thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Adding phosphate to protein
can you be a bit more specific? Are you expecting to phosphorylate the protein along the trajectory or did you want to run continuous simulations with different phosphorylation states? On 2012-09-03 09:30:58AM +0200, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want to add a phosphate to my protein. Is this possible with gromacs? Thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Adding phosphate to protein
Hi, I have my protein without phosphorylations and now I want to phosphorylate one residue of my protein. Is this possible? Thank you can you be a bit more specific? Are you expecting to phosphorylate the protein along the trajectory or did you want to run continuous simulations with different phosphorylation states? On 2012-09-03 09:30:58AM +0200, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want to add a phosphate to my protein. Is this possible with gromacs? Thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst| KAUL 752A Genetics, Div. of Research| 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808| == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Adding phosphate to protein
You haven't anwsered my question. Did you just want to add the phosphate before starting the simulation or were you hoping for the simulation to do it for you? On 2012-09-03 09:51:12AM +0200, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi, I have my protein without phosphorylations and now I want to phosphorylate one residue of my protein. Is this possible? Thank you can you be a bit more specific? Are you expecting to phosphorylate the protein along the trajectory or did you want to run continuous simulations with different phosphorylation states? On 2012-09-03 09:30:58AM +0200, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want to add a phosphate to my protein. Is this possible with gromacs? Thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] puzzling about ffnonbonded.itp
Dear gmxers, While I try to make one customed force field by studying some existing force fields, I find that bond_type and at.num defining [atomtypes ] in the ffnonbonded.itp are included in some force fields (i.e. oplsaa), but not in other force fields (i.e gmx). I wonder how gmx identifies the difference and choose the correct parameters from them. Could you please expain this in details? Thank you very much for any reply. Yours sincerely, Chaofu Wu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Adding phosphate to protein
I want to add the phosphor first. And I hoped that there is a program just like the pdb2gmx which adds hydrogens to the protein. You haven't anwsered my question. Did you just want to add the phosphate before starting the simulation or were you hoping for the simulation to do it for you? On 2012-09-03 09:51:12AM +0200, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi, I have my protein without phosphorylations and now I want to phosphorylate one residue of my protein. Is this possible? Thank you can you be a bit more specific? Are you expecting to phosphorylate the protein along the trajectory or did you want to run continuous simulations with different phosphorylation states? On 2012-09-03 09:30:58AM +0200, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want to add a phosphate to my protein. Is this possible with gromacs? Thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst| KAUL 752A Genetics, Div. of Research| 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808| == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Adding phosphate to protein
You'll have to do it manually. Perhaps VMD or Chimera can help you with adding the atoms to the initial pdb. Then you'll have to create a modified amino acid topology for the amino acid that is getting phosphorylated in your forcefield's .rtp file. On 2012-09-03 10:05:08AM +0200, reising...@rostlab.informatik.tu-muenchen.de wrote: I want to add the phosphor first. And I hoped that there is a program just like the pdb2gmx which adds hydrogens to the protein. You haven't anwsered my question. Did you just want to add the phosphate before starting the simulation or were you hoping for the simulation to do it for you? On 2012-09-03 09:51:12AM +0200, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi, I have my protein without phosphorylations and now I want to phosphorylate one residue of my protein. Is this possible? Thank you can you be a bit more specific? Are you expecting to phosphorylate the protein along the trajectory or did you want to run continuous simulations with different phosphorylation states? On 2012-09-03 09:30:58AM +0200, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want to add a phosphate to my protein. Is this possible with gromacs? Thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Turning off electrostatics between groups using custom tables?
2 sep 2012 kl. 20.47 skrev Smitty: 1) That .mdp applies different tables to K-K, protein-protein and all other interactions, which isn't what you've said you've done. 3) Your life will be simpler if you use energygrp_table only for the group-group interactions you want to change, and leave the default interactions normal. It will also be faster, because using tabulated interactions is much slower than the normal ones. Mark -- gmx-users mailing listgmx-users@ http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request@. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Thanks mark, I have since gone back and modified the .mdp file after re-reading the tutorial and manual and have come up with the new attached .mdp file ( http://gromacs.5086.n6.nabble.com/file/n5000746/md.mdp md.mdp , which I think removes the problems you highlighted in 1) and 3). I no longer have an exploding system; however, when I run g_energy on the output .edr file from a short run (looking at the K+ and protein energy groups) I get the following output: Energy Average RMSD Fluct. Drift Tot-Drift --- Coul-SR:K+-K+551.07208.16289.62870.69831 650.828 LJ-SR:K+-K+ 1.43168 0.794798 0.668453 0.00159813 1.48946 Coul-14:K+-K+ 0 0 0 0 0 LJ-14:K+-K+ 0 0 0 0 0 Coul-SR:K+-Protein -6994.99 1978.51003.44 -6.33779 -5906.85 LJ-SR:K+-Protein52.344713.739811.2697 0.0292135 27.2271 Coul-14:K+-Protein0 0 0 0 0 LJ-14:K+-Protein 0 0 0 0 0 Coul-SR:Protein-Protein-246.63943.9503 30.2460.11852 110.461 LJ-SR:Protein-Protein -81.920910.20869.29929 0.0156543 14.5899 Coul-14:Protein-Protein 1477.9119.769316.2154 -0.0420325 -39.1745 LJ-14:Protein-Protein 158.21911.145510.5729 -0.0131077 -12.2164 Which is closer to what I am going for, but I would expect that the Coul-14/LJ-14 K+-K+ would not be zero. Any ideas on what I am still not doing correct? Thanks for all the help. Why would you have 1-4 interactions for monoatomic species? Or between different molecules for that matter? -- View this message in context: http://gromacs.5086.n6.nabble.com/Turning-off-electrostatics-between-groups-using-custom-tables-tp5000723p5000746.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_mindist - reg
On 9/3/12 2:04 AM, Raj wrote: hi all, I would like to measure the hydrophobic interaction of the ligand against the protein during the simulation . From the forum I learnt g_mindist will be the better tool. But when i used the command g_mindist -f traj.xtc -s topol.tpr -n index.ndx -on numcont.xvg -group and selected protein as group1 and ligand as group 2 i get the result like this g_mindist -f traj.xtc -s pull.tpr -n index.ndx -on numcont.xvg -group # # g_mindist is part of G R O M A C S: # # Good ROcking Metal Altar for Chronical Sinners # @title Number of Contacts 0.6 nm @xaxis label Time (ps) @yaxis label Number @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend Protein-UNK 0.00e+0021 1.00e+0021 2.00e+0021 3.00e+0021 4.00e+0021 5.00e+0021 6.00e+0021 7.00e+0021 8.00e+0021 9.00e+0021 1.00e+0121 1.10e+0121 1.20e+0121 1.30e+0121 1.40e+0121 1.50e+0121 1.60e+0121 1.70e+0121 1.80e+0121 1.90e+0121 2.00e+0121 2.10e+0121 2.20e+0121 2.30e+0121 2.40e+0121 2.50e+0121 2.60e+0121 2.70e+0121 2.80e+0121 2.90e+0121 3.00e+0121 3.10e+0121 3.20e+0121 3.30e+0121 3.40e+0121 3.50e+0121 3.60e+0121 3.70e+0121 3.80e+0121 3.90e+0121 4.00e+0121 4.10e+0121 4.20e+0121 4.30e+0121 4.40e+0121 4.50e+0121 4.60e+0121 4.70e+0121 4.80e+0121 4.90e+0121 5.00e+0121 5.10e+0121 5.20e+0121 5.30e+0121 I would like to know what ever the data I've obtained is the number of hydrophobic interaction between the ligand and protein or I am wrong somewhere. Please help me. Thanks in advance If the index groups contain hydrophobic atoms, then yes. If they contain other atoms, then no. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_tune_pme cannot be executed
Hi Zifeng, have you tried to use g_tune_pme -npstring none … Carsten On Aug 20, 2012, at 5:07 PM, zifeng li lizife...@gmail.com wrote: Dear Gromacs users, Morning! I am using Gromacs 4.5.4 version and tries to use the magic power of g_tune_pme. However, it cannot be executed with the error in benchtest.log file: mpirun error: do not specify a -np argument. it is set for you. The cluster I use needs to submit mpirun job though PBS script, which looks like following: #PBS -l nodes=8 #PBS -l walltime=2:00:00 #PBS -l pmem=2gb cd $PBS_O_WORKDIR # echo echo echo Job started on `hostname` at `date` g_tune_pme -s npt echo echo Job Ended at `date` echo ~ I can run the command mpirun mdrun_mpi -deffnm npt using this PBS script before and as you notice, -np for g_tune_mpe is not used. Any suggestions about this issue? What I have tried for your reference: 1. to delete the first line. well...it won't help. 2. to set the environmental variable as Manual suggests curiously: export MPIRUN=/usr/local/mpirun -machinefile hostsuse my account name as the hosts here. Thanks in advance! Good day :) -Zifeng -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www3.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_tune_pme for multiple nodes
Hi Chandan, g_tune_pme also finds the optimal number of PME cores if the cores are distributed on multiple nodes. Simply pass the total number of cores to the -np option. Depending on the MPI and queue environment that you use, the distribution of the cores over the nodes may have to be specified in a hostfile / machinefile. Check g_tune_pme -h on how to set that. Best, Carsten On Aug 28, 2012, at 8:33 PM, Chandan Choudhury iitd...@gmail.com wrote: Dear gmx users, I am using 4.5.5 of gromacs. I was trying to use g_tune_pme for a simulation. I intend to execute mdrun at multiple nodes with 12 cores each. Therefore, I would like to optimize the number of pme nodes. I could execute g_tune_pme -np 12 md.tpr. But this will only find the optimal PME nodes for single nodes run. How do I find the optimal PME nodes for multiple nodes. Any suggestion would be helpful. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www3.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] au virtual atom
On 9/3/12 2:45 AM, fatemeh ramezani wrote: Thanks for your response, but I've read the manual. What I realized is that, for example, I should consider for every two, three or … atoms, a virtual atom. Here are some questions: 1 - Does not important consider which atoms together? or How much is the angle between atoms? 2 -Does I need to manually sort atoms and consider for every group a virtual site? You have yet to really state what the nature of the virtual site(s) is. A virtual site is constructed by the positions of some amount of atoms, and the exact geometry of that construction depends upon where the virtual site(s) should be. How many sites do you need? Where are they in relation to other atoms? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to optimize performance of IBM Power 775?
Hi Albert, On Aug 25, 2012, at 7:37 AM, Albert mailmd2...@gmail.com wrote: Dear: Our institute got a IBM Power 775 cluster and it claimed to be very good. However, it doesn't support g_tune_pme. Are you shure that it is not supported? Maybe you just need the right syntax. I use the following script for job submission: #@ job_name = gromacs_job #@ output = gromacs.out #@ error = gromacs.err #@ class = kdm #@ node = 4 #@ tasks_per_node = 32 #@ wall_clock_limit = 01:00:00 #@ network.MPI = sn_all,not_shared,US,HIGH #@ notification = never #@ environment = COPY_ALL #@ job_type = parallel #@ queue mpiexec -n 128 /opt/gromacs/4.5.5/bin/mdrun -nosum -dlb yes -v -s md.tpr it is only 7 ns/day. However, in another cluster with the same system, Core number and parameters, I can get up to 30 ns/day. Does anybody have any advices for this issue? On a Power6 machine, I have successfully used the following job file: # @ shell=/bin/ksh # # Sample script for LoadLeveler # # @ error = run_1.err.$(jobid) # @ output = run_1.out.$(jobid) # @ job_type = parallel # @ environment= COPY_ALL # @ node_usage= not_shared # @ node = 1 # @ tasks_per_node = 4 # @ resources = ConsumableCpus(1) # @ network.MPI = sn_all,not_shared,us # @ wall_clock_limit = 0:05:00 # @ notification = complete # @ queue # # run the program # export MDRUN=/path/to/gromacs-4.5.1/bin/mdrun_mpi export MPIRUN=poe #no poe here! /path/to/g_tune_pme -np 4 \ -npstring none -s ./ap.tpr -resetstep 1 -steps 10 Hope that helps, Carsten thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www3.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: g_mindist - reg
thank you justin ... I have given the entire protein as one group.. now will it be ok or i need to give only hydrophobic resides alone as a index group. Thank you once again for yor response -- View this message in context: http://gromacs.5086.n6.nabble.com/g-mindist-reg-tp5000756p5000771.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_mindist - reg
On 9/3/12 7:47 AM, Raj wrote: thank you justin ... I have given the entire protein as one group.. now will it be ok or i need to give only hydrophobic resides alone as a index group. Thank you once again for yor response If you want hydrophobic contacts, you need index groups that specify hydrophobic atoms, otherwise you're getting all contacts - polar and nonpolar - in the calculated quantity. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] puzzling about ffnonbonded.itp
On 3/09/2012 6:02 PM, Wu Chaofu wrote: Dear gmxers, While I try to make one customed force field by studying some existing force fields, I find that bond_type and at.num defining [atomtypes ] in the ffnonbonded.itp are included in some force fields (i.e. oplsaa), but not in other force fields (i.e gmx). I wonder how gmx identifies the difference and choose the correct parameters from them. Could you please expain this in details? Thank you very much for any Not sure which part of these issues you're concerned about. Different force fields work differently. Few of these fields are actually relevant (e.g. charge never is, in practice), some get over-ridden some times. grompp has a bunch of magic scanf() format strings that work out what is in each field and dispatches the information to the data structure correctly. In practice, you should probably pick an existing force field as a model and follow its format. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Turning off electrostatics between groups using custom tables?
Erik Marklund wrote 2 sep 2012 kl. 20.47 skrev Smitty: Why would you have 1-4 interactions for monoatomic species? Or between different molecules for that matter? --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 erikm@.uu http://www2.icm.uu.se/molbio/elflab/index.html Thanks Erik, I don't know what I was thinking. However, when I was checking for consistency between K+K+ dynamics for the table-based run and my standard run, I find that my radial distribution functions are significantly different? Attached are two examples (.xvg) http://gromacs.5086.n6.nabble.com/file/n5000778/rdf_K%2BK%2B_fromtablerun.xvg rdf_K+K+_fromtablerun.xvg http://gromacs.5086.n6.nabble.com/file/n5000778/rdf_K%2BK%2B_fromstdrun.xvg rdf_K+K+_fromstdrun.xvg . So it seems I am still have some problems. Thanks to both you and mark for all of the help. -Smitty -- View this message in context: http://gromacs.5086.n6.nabble.com/Turning-off-electrostatics-between-groups-using-custom-tables-tp5000723p5000778.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
AW: [gmx-users] Adding phosphate to protein
There is a G43a1 modification available with phosphorylated amino acids in the users contribution section of the Gromacs homepage. http://www.gromacs.org/Downloads/User_contributions/Force_fields It was uploaded by Graham Smith and Justin made it compatible with the Gromacs 4.5.x versions, so maybe this would be a good starting point for your modified residue. Good luck. -Ursprüngliche Nachricht- Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im Auftrag von reising...@rostlab.informatik.tu-muenchen.de Gesendet: Montag, 3. September 2012 10:07 An: Discussion list for GROMACS users Betreff: Re: [gmx-users] Adding phosphate to protein I want to add the phosphor first. And I hoped that there is a program just like the pdb2gmx which adds hydrogens to the protein. You haven't anwsered my question. Did you just want to add the phosphate before starting the simulation or were you hoping for the simulation to do it for you? On 2012-09-03 09:51:12AM +0200, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi, I have my protein without phosphorylations and now I want to phosphorylate one residue of my protein. Is this possible? Thank you can you be a bit more specific? Are you expecting to phosphorylate the protein along the trajectory or did you want to run continuous simulations with different phosphorylation states? On 2012-09-03 09:30:58AM +0200, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want to add a phosphate to my protein. Is this possible with gromacs? Thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst| KAUL 752A Genetics, Div. of Research| 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808| == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Is there a way to redirect utility output to the screen, rather than to a file?
Hi, Sometimes, I want to take a quick look at a certain property using one of the Gromacs utilities. For example, I might want to use: g_traj -f traj.trr -s topol.tpr -n index.ndx -nox -noy -b 5 -e 10 -ox coord.xvg to look at the z-component of the group specified in index.ndx from t = 5 ps to 10 ps. I can save this data in an .xvg file (coord.xvg) using the -ox switch. However, what if I would rather not save the data to an .xvg file (since I just want to take a quick look)? Does anyone know if it is possible to redirect the output of g_traj to the screen, rather than to coord.xvg? Thank you so much for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Is there a way to redirect utility output to the screen, rather than to a file?
Have you tried to write to a named pipe? Like mkfifo coord.xvg then g_traj -ox coord.xvg? Then tail -F coord.xvg? I'm not sure this is less work than just letting it write the xvg and then looking at the xvg (and deleting it later)... On 2012-09-03 08:26:56PM -0400, Andrew DeYoung wrote: Hi, Sometimes, I want to take a quick look at a certain property using one of the Gromacs utilities. For example, I might want to use: g_traj -f traj.trr -s topol.tpr -n index.ndx -nox -noy -b 5 -e 10 -ox coord.xvg to look at the z-component of the group specified in index.ndx from t = 5 ps to 10 ps. I can save this data in an .xvg file (coord.xvg) using the -ox switch. However, what if I would rather not save the data to an .xvg file (since I just want to take a quick look)? Does anyone know if it is possible to redirect the output of g_traj to the screen, rather than to coord.xvg? Thank you so much for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
