Re: [gmx-users] calculation radial concentration plots
Hi, Check out RIcard Lavery's CANION, I think it'll do what you need. There's the paper http://nar.oxfordjournals.org/content/early/2014/06/06/nar.gku504.full And the software https://bisi.ibcp.fr/tools/curves_plus/canion-user-guide.html Felipe On 01/07/15 09:31, soumadwip ghosh wrote: Hi all, I have been asked by one of my reviewers to calculate the number of excess cations surrounding a DNA duplex using radial concentration of the ions computed by integrating the grid-based concentration data within a cylindrical volume surrounding the DNA . I am actually trying to obtain curves like that of figure 7 in the link below- http://onlinelibrary.wiley.com/doi/10.1002/bip.22461/epdf Which are obtained from the radial concentration profiles. My question is how to make a radial concentration profile of say tetramethylammonium cations from some DNA groove/ backbone atoms and then obtain curves like that of figure 7 using equation 2 of the above reference. Thanks for your help in advance. Soumadwip Ghosh Research Fellow IITB India. -- Felipe Merino Max Planck Institute for Molecular Physiology Department of Structural Biochemistry Otto-Hahn-Str. 11 44227 Dortmund Phone: +49 231 133 2306 -- 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] g_rdf
Dear Gromacs users, I have a problem with g_rdf. I try to calculate the rdf function for two groups: 1. Oxygen atom of one water molecule; 2. Oxygen atoms of all other water molecules in the box; When I use different number of frames from the trajectory I get very different rdf plots. First peak (round 0.26 nm) varies from 3.9 to 18 g(r). If I am not mistaken, this number related to the coordination number of water and should be found 3.8-4 in any case. Why there is such strong difference? Is there a problem with time averaging? I get the same problem if initially prepare the short versions of the trajectory for g_rdf input gmx rdf, VERSION 5.0.4 g_rdf -f traj.xtc -s md.tpr -o rdf_0to1000frame.xvg -n index.ndx -b 0 -e 100 g_rdf -f traj.xtc -s md.tpr -o rdf_0to1000frame.xvg -n index.ndx -b 0 -e 1000 g_rdf -f traj.xtc -s md.tpr -o rdf_0to1000frame.xvg -n index.ndx -b 0 -e 5000 g_rdf -f traj.xtc -s md.tpr -o rdf_0to1000frame.xvg -n index.ndx -b 0 -e 1 png plot is attached Thank you -- Sincerely, Yulian Gavrilov -- 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] patched version installation for free energy
On 7/1/15 1:05 PM, Ahmet Yıldırım wrote: I am already trying to install it into a separate directory. Source files is in the gromacs-patched folder. I created gromacs directory away from $HOME/Public/gromacs-patched. And you get the same error, even after starting from a fresh build directory? -Justin 2015-07-01 18:56 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 7/1/15 12:52 PM, Ahmet Yıldırım wrote: Hi, When I install the patched GROMACS version ( https://github.com/gromacs/gromacs/tree/022ad08b2fd0c1de085e88ac81a61841c4daea9c ) on cluster, I get the following error after command-2. Why do I get this error? Command-1: t-mn01 [~/Public/gromacs]$ cmake ../gromacs-patched -DGMX_GPU=OFF -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/a/user/Public/gromacs Don't install into the source tree. -Justin -- Configuring done -- Generating done -- Build files have been written to: /home/a/user/Public/gromacs Command-2: t-mn01 [~/Public/gromacs]$ make -j 8 install -- Installing: /home/a/user/Public/gromacs/include/gromacs/trajectoryanalysis/cmdlinerunner.h CMake Error at src/programs/cmake_install.cmake:42 (FILE): file INSTALL cannot find /home/a/user/Public/gromacs/bin/gmx_mpi. Call Stack (most recent call first): src/cmake_install.cmake:40 (INCLUDE) cmake_install.cmake:44 (INCLUDE) make: *** [install] Error 1 -- == 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.
[gmx-users] pdb2gmx warning residue mapping
Dear all, when i run pdb2gmx -f name.pdb with charmm27 and tip3 water model for my structure i got an warning: Residue 1 named GLN of a molecule in the input file was mapped to an entry in the topology database,but the atom CA used in that entry is not found in the input file.Perhaps your atom and reside naming needs to be fixed. when i checked my structure for four or five times i couldnt find any problem atom CA which is defined in charmm27 still why this error. how to solve this error or if i avoid and proceed it will make problem during minimization and md? here is GLN entry ATOM 42 CD2 LEU A 6 -7.733 -2.176 0.996 1.00 0.00 C ATOM 43 CA GLN A 1 -3.232 3.298 -0.224 1.00 0.00 C ATOM 44 CB GLN A 1 -4.479 3.910 0.508 1.00 0.00 C ATOM 45 CG GLN A 1 -4.699 5.392 0.155 1.00 0.00 C ATOM 46 CD GLN A 1 -6.125 5.743 0.501 1.00 0.00 C ATOM 47 NZ GLN A 1 -6.625 7.021 0.232 1.00 0.00 N ATOM 48 OD GLN A 1 -6.886 4.863 0.922 1.00 0.00 O ATOM 49 HN GLN A 1 -2.342 1.326 0.325 1.00 0.00 H ATOM 50 HN LEU A 2 -1.012 3.459 -1.579 1.00 0.00 H ATOM 51 HN LYS A 3 0.953 2.002 -0.768 1.00 0.00 H ATOM 52 HN ALA A 4 1.202 -0.067 -0.562 1.00 0.00 H ATOM 53 HN LEU A 6 -2.606 -0.728 0.937 1.00 0.00 H ATOM 54 HN LYS A 5 -0.672 -1.114 0.652 1.00 0.00 H ATOM 55 HA LEU A 2 0.683 5.077 -1.474 1.00 0.00 H -- 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] calculation radial concentration plots
Thanks for an early reply. In the link provided I can see that CANION requires an Amber output file whereas my output files are GROMACS generated and I used CHARMM 27 force field for carrying out md simulations. Another thing is that I am a newbie in computational studies and I really dont know how to use such codes and programs. Is there anything (may be in connection with g_rdf and g_select ) which can serve my purpose? I am obviously keeping CANION in mind but it would be more helpful if some alternative may be suggested. Thanks and regards Soumadwip Research Fellow, IITB 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] Creating custom position restraints for a multi-chain protein
Here's the solution I came up with, for posterity. My protein has four chains, two of each type. I left the first chain alone, since gromacs handles it just fine, but pulled out the second chain into its own PDB and renumbered the atoms: gmx make_ndx -f protein.pdb -o chain-b.ndx del 0-9 chain b q gmx editconf -f protein.pdb -n chain-b.ndx -o chain-b1.pdb gmx genconf -f chain-b1.pdb -o chain-b.pdb -renumber This can be done as many times as needed for as many types of chains as there are. I then created indices for the parts of the protein I wanted restrained: gmx make_ndx -f protein.pdb -o struc-a.ndx del 0-9 r x-y | r z-w | ... | r n-m chain a [SEE NOTE BELOW] name 0 StructureA q gmx make_ndx -f chain-b.pdb -o struc-b.ndx del 0-9 r a-b | r c-d | ... | r i-j name 0 StructureB q Again, this can be done more than twice if needed. If the residue numbering in your PDB file doesn't start over at 1 for each chain, you can leave off the chain x part. Finally, I generated the restraints, and made copies using the command line (BACK UP THE ORIGINAL POSRE ITP FILES, JUST IN CASE): gmx genrestr -f protein.pdb -n struc-a.ndx -o posre_Protein_chain_A.itp gmx genrestr -f chain-b.pdb -n struc-b.ndx -o posre_Protein_chain_B.itp cp posre_Protein_chain_A.itp posre_Protein_chain_C.itp cp posre_Protein_chain_B.itp posre_Protein_chain_D.itp You don't need to make copies if you don't have symmetrical units in your protein. I hope this helps others who run into a similar issue with renumbering atoms in .itp files. 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: Tuesday, June 30, 2015 6:01 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Creating custom position restraints for a multi-chain protein On 6/30/15 5:42 PM, Kolmus, Elizabeth K. wrote: Are there any plans to address this in future releases? I realize you already have enough work on your plate to last you for years, but I can't be the only person wanting to treat some portions of a multimeric molecule differently than others. Anyone is welcome to submit a feature request on redmine.gromacs.org (or even better, help write the code!) but this would remain a very low priority for the dev team unless someone is really enthusiastic about it. The tool is stated to be pretty much a uni-tasker, and there are several workarounds for multimeric systems (modify the .itp files that pdb2mgx writes, separate the coordinates and process them individually, clever use of awk, etc). -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] DNA virtual site with Charmm force field
Hi Erik, Thanks. I'll try work them out. Regards Terry On Wed, Jul 1, 2015 at 7:29 PM, Erik Marklund erik.markl...@chem.ox.ac.uk wrote: Hi Terry, Correct. The forcefields provided with gromacs do not have a complete set of parameters for making vsites for nucleotides. You can work them out from geometry and mass moments however. Kind regards, Erik On 1 Jul 2015, at 10:23, Terry terrence...@gmail.com wrote: Hi all, I'm trying to use virtual sites in a DNA in water simulation with Charmm27 force field. When feeding my pdb to pdb2gmx with this cammand pdb2gmx -f my_DNA.pdb -vsite hydrogens', it gives me this error Fatal error: No vsite database NH2 entry for type NN1 Is this not implemented or did I miss something? Any input would be appreciated. Regards Terry -- 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] DNA virtual site with Charmm force field
Hi all, I'm trying to use virtual sites in a DNA in water simulation with Charmm27 force field. When feeding my pdb to pdb2gmx with this cammand pdb2gmx -f my_DNA.pdb -vsite hydrogens', it gives me this error Fatal error: No vsite database NH2 entry for type NN1 Is this not implemented or did I miss something? Any input would be appreciated. Regards Terry -- 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-DNA simulation LINKS error
Thanks for the advice, Justin and Mark. After rerunning the simulation with guanine in the DNA I've found no noticeable problems. Now I'm looking for another possible sources for mistakes. 1.The input PDB file is formatted using amber conventions, i.e. DG5 and DG3 for terminal guanosine residues, CYX for S--S linked cystine and so on. Could it result in any erroneous interpretations by pdb2gmx? 2. I think I correctly created 8-oxoguanine entry in amber force field files by copying and modifying existing one for normal guanine, but I want to re-check myself just to be sure. Is there anything more in-depth available than rather laconic instruction from the GROMACS site? I've tried searching through the maillist, but looks like nothing similar came up (It's a pity that no forum exist, looking for past answers would be far simpler). 3. Could an accidental simultaneous execution of two or three jobs on one workstation (scheduling script was set incorrectly once) cause LINKS errors? -- 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-DNA simulation LINKS error
On 7/1/15 8:08 AM, Timofey Tyugashev wrote: Thanks for the advice, Justin and Mark. After rerunning the simulation with guanine in the DNA I've found no noticeable problems. Now I'm looking for another possible sources for mistakes. 1.The input PDB file is formatted using amber conventions, i.e. DG5 and DG3 for terminal guanosine residues, CYX for S--S linked cystine and so on. Could it result in any erroneous interpretations by pdb2gmx? pdb2gmx throws obvious errors if there is a problem. AMBER uses unique nomenclature for termini, which is consistent with what you describe here. 2. I think I correctly created 8-oxoguanine entry in amber force field files by copying and modifying existing one for normal guanine, but I want to re-check myself just to be sure. Is there anything more in-depth available than rather laconic instruction from the GROMACS site? I've tried searching through the maillist, but looks like nothing similar came up (It's a pity that no forum exist, looking for past answers would be far simpler). Generating force field parameters is well beyond the scope of what is or should be included in GROMACS documentation. We provide a few resources in terms of the implementation, but given the vast scope of this topic, and the expert knowledge required, it is impossible to teach people to derive parameters suitably. For that, you need to read and understand the literature regarding the parametrization theory and methods of your chosen force field. At least you've arrived at your answer - you have sub-optimal parameters for 8-oxoG that cause a crash. Now the task is to derive parameters of suitable quality. 3. Could an accidental simultaneous execution of two or three jobs on one workstation (scheduling script was set incorrectly once) cause LINKS errors? No. Independent mdrun process do not affect each other. -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] (no subject)
On 7/1/15 12:54 AM, RINU KHATTRI wrote: Hello gromacs users i am working on membrane protein with complex i want to calculate the distance of a particular amino acid to ligand in all simulation time period if g_dist is the answer i didn't get the desired output . kindly help There's nothing anyone can do to help a complaint of didn't get the desired output. What was your command? What was your output? Why don't you think that's right? g_dist measures distances; it is what you need to use, provided you use it correctly. -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] Error in volume coupling, no domain decomposition
On 7/1/15 12:52 AM, shabana yasmeen wrote: I have used mdrun -nt 1.. can anyone guide me that Is this command doing volume couling and after this command is there any need to do volume coupling again??? mdrun does whatever you tell it. The .mdp settings dictate the physics, ensemble, etc. -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] DNA virtual site with Charmm force field
Hi Terry, Correct. The forcefields provided with gromacs do not have a complete set of parameters for making vsites for nucleotides. You can work them out from geometry and mass moments however. Kind regards, Erik On 1 Jul 2015, at 10:23, Terry terrence...@gmail.com wrote: Hi all, I'm trying to use virtual sites in a DNA in water simulation with Charmm27 force field. When feeding my pdb to pdb2gmx with this cammand pdb2gmx -f my_DNA.pdb -vsite hydrogens', it gives me this error Fatal error: No vsite database NH2 entry for type NN1 Is this not implemented or did I miss something? Any input would be appreciated. Regards Terry -- 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] pdb2gmx warning residue mapping
On 7/1/15 2:13 PM, Nikhil wrote: Dear all, when i run pdb2gmx -f name.pdb with charmm27 and tip3 water model for my structure i got an warning: Residue 1 named GLN of a molecule in the input file was mapped to an entry in the topology database,but the atom CA used in that entry is not found in the input file.Perhaps your atom and reside naming needs to be fixed. when i checked my structure for four or five times i couldnt find any problem atom CA which is defined in charmm27 still why this error. how to solve this error or if i avoid and proceed it will make problem during minimization and md? here is GLN entry ATOM 42 CD2 LEU A 6 -7.733 -2.176 0.996 1.00 0.00 C ATOM 43 CA GLN A 1 -3.232 3.298 -0.224 1.00 0.00 C ATOM 44 CB GLN A 1 -4.479 3.910 0.508 1.00 0.00 C ATOM 45 CG GLN A 1 -4.699 5.392 0.155 1.00 0.00 C ATOM 46 CD GLN A 1 -6.125 5.743 0.501 1.00 0.00 C ATOM 47 NZ GLN A 1 -6.625 7.021 0.232 1.00 0.00 N ATOM 48 OD GLN A 1 -6.886 4.863 0.922 1.00 0.00 O ATOM 49 HN GLN A 1 -2.342 1.326 0.325 1.00 0.00 H ATOM 50 HN LEU A 2 -1.012 3.459 -1.579 1.00 0.00 H ATOM 51 HN LYS A 3 0.953 2.002 -0.768 1.00 0.00 H ATOM 52 HN ALA A 4 1.202 -0.067 -0.562 1.00 0.00 H ATOM 53 HN LEU A 6 -2.606 -0.728 0.937 1.00 0.00 H ATOM 54 HN LYS A 5 -0.672 -1.114 0.652 1.00 0.00 H ATOM 55 HA LEU A 2 0.683 5.077 -1.474 1.00 0.00 H You're missing all kinds of atoms. This coordinate file is pretty hopeless. -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] patched version installation for free energy
On 7/1/15 12:52 PM, Ahmet Yıldırım wrote: Hi, When I install the patched GROMACS version ( https://github.com/gromacs/gromacs/tree/022ad08b2fd0c1de085e88ac81a61841c4daea9c) on cluster, I get the following error after command-2. Why do I get this error? Command-1: t-mn01 [~/Public/gromacs]$ cmake ../gromacs-patched -DGMX_GPU=OFF -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/a/user/Public/gromacs Don't install into the source tree. -Justin -- Configuring done -- Generating done -- Build files have been written to: /home/a/user/Public/gromacs Command-2: t-mn01 [~/Public/gromacs]$ make -j 8 install -- Installing: /home/a/user/Public/gromacs/include/gromacs/trajectoryanalysis/cmdlinerunner.h CMake Error at src/programs/cmake_install.cmake:42 (FILE): file INSTALL cannot find /home/a/user/Public/gromacs/bin/gmx_mpi. Call Stack (most recent call first): src/cmake_install.cmake:40 (INCLUDE) cmake_install.cmake:44 (INCLUDE) make: *** [install] Error 1 -- == 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] patched version installation for free energy
I am already trying to install it into a separate directory. Source files is in the gromacs-patched folder. I created gromacs directory away from $HOME/Public/gromacs-patched. 2015-07-01 18:56 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 7/1/15 12:52 PM, Ahmet Yıldırım wrote: Hi, When I install the patched GROMACS version ( https://github.com/gromacs/gromacs/tree/022ad08b2fd0c1de085e88ac81a61841c4daea9c ) on cluster, I get the following error after command-2. Why do I get this error? Command-1: t-mn01 [~/Public/gromacs]$ cmake ../gromacs-patched -DGMX_GPU=OFF -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/a/user/Public/gromacs Don't install into the source tree. -Justin -- Configuring done -- Generating done -- Build files have been written to: /home/a/user/Public/gromacs Command-2: t-mn01 [~/Public/gromacs]$ make -j 8 install -- Installing: /home/a/user/Public/gromacs/include/gromacs/trajectoryanalysis/cmdlinerunner.h CMake Error at src/programs/cmake_install.cmake:42 (FILE): file INSTALL cannot find /home/a/user/Public/gromacs/bin/gmx_mpi. Call Stack (most recent call first): src/cmake_install.cmake:40 (INCLUDE) cmake_install.cmake:44 (INCLUDE) make: *** [install] Error 1 -- == 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. -- Ahmet Yıldırım -- 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] patched version installation for free energy
:) yes. 2015-07-01 19:08 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 7/1/15 1:05 PM, Ahmet Yıldırım wrote: I am already trying to install it into a separate directory. Source files is in the gromacs-patched folder. I created gromacs directory away from $HOME/Public/gromacs-patched. And you get the same error, even after starting from a fresh build directory? -Justin 2015-07-01 18:56 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 7/1/15 12:52 PM, Ahmet Yıldırım wrote: Hi, When I install the patched GROMACS version ( https://github.com/gromacs/gromacs/tree/022ad08b2fd0c1de085e88ac81a61841c4daea9c ) on cluster, I get the following error after command-2. Why do I get this error? Command-1: t-mn01 [~/Public/gromacs]$ cmake ../gromacs-patched -DGMX_GPU=OFF -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/a/user/Public/gromacs Don't install into the source tree. -Justin -- Configuring done -- Generating done -- Build files have been written to: /home/a/user/Public/gromacs Command-2: t-mn01 [~/Public/gromacs]$ make -j 8 install -- Installing: /home/a/user/Public/gromacs/include/gromacs/trajectoryanalysis/cmdlinerunner.h CMake Error at src/programs/cmake_install.cmake:42 (FILE): file INSTALL cannot find /home/a/user/Public/gromacs/bin/gmx_mpi. Call Stack (most recent call first): src/cmake_install.cmake:40 (INCLUDE) cmake_install.cmake:44 (INCLUDE) make: *** [install] Error 1 -- == 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. -- Ahmet Yıldırım -- 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] patched version installation for free energy
Hi, When I install the patched GROMACS version ( https://github.com/gromacs/gromacs/tree/022ad08b2fd0c1de085e88ac81a61841c4daea9c) on cluster, I get the following error after command-2. Why do I get this error? Command-1: t-mn01 [~/Public/gromacs]$ cmake ../gromacs-patched -DGMX_GPU=OFF -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/a/user/Public/gromacs -- Configuring done -- Generating done -- Build files have been written to: /home/a/user/Public/gromacs Command-2: t-mn01 [~/Public/gromacs]$ make -j 8 install -- Installing: /home/a/user/Public/gromacs/include/gromacs/trajectoryanalysis/cmdlinerunner.h CMake Error at src/programs/cmake_install.cmake:42 (FILE): file INSTALL cannot find /home/a/user/Public/gromacs/bin/gmx_mpi. Call Stack (most recent call first): src/cmake_install.cmake:40 (INCLUDE) cmake_install.cmake:44 (INCLUDE) make: *** [install] Error 1 -- Ahmet Yıldırım -- 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] calculation radial concentration plots
Hi all, I have been asked by one of my reviewers to calculate the number of excess cations surrounding a DNA duplex using radial concentration of the ions computed by integrating the grid-based concentration data within a cylindrical volume surrounding the DNA . I am actually trying to obtain curves like that of figure 7 in the link below- http://onlinelibrary.wiley.com/doi/10.1002/bip.22461/epdf Which are obtained from the radial concentration profiles. My question is how to make a radial concentration profile of say tetramethylammonium cations from some DNA groove/ backbone atoms and then obtain curves like that of figure 7 using equation 2 of the above reference. Thanks for your help in advance. Soumadwip Ghosh Research Fellow IITB 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] gromacs.org_gmx-users Digest, Vol 135, Issue 5
No, I may have misleadingly phrased my question but I do use 8-oxoguanosine parameters calculated and published in a paper for AMBER years ago. I am simply worried about correctly formatting them into force field definition files in GROMACS. A far simpler task than calculating and verifying the numbers themselves all by myself. 01.07.2015 18:51, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет: -- Message: 6 Date: Wed, 01 Jul 2015 08:41:09 -0400 From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Protein-DNA simulation LINKS error Message-ID: 5593dfe5.20...@vt.edu Content-Type: text/plain; charset=windows-1252; format=flowed On 7/1/15 8:08 AM, Timofey Tyugashev wrote: Thanks for the advice, Justin and Mark. After rerunning the simulation with guanine in the DNA I've found no noticeable problems. Now I'm looking for another possible sources for mistakes. 1.The input PDB file is formatted using amber conventions, i.e. DG5 and DG3 for terminal guanosine residues, CYX for S--S linked cystine and so on. Could it result in any erroneous interpretations by pdb2gmx? pdb2gmx throws obvious errors if there is a problem. AMBER uses unique nomenclature for termini, which is consistent with what you describe here. 2. I think I correctly created 8-oxoguanine entry in amber force field files by copying and modifying existing one for normal guanine, but I want to re-check myself just to be sure. Is there anything more in-depth available than rather laconic instruction from the GROMACS site? I've tried searching through the maillist, but looks like nothing similar came up (It's a pity that no forum exist, looking for past answers would be far simpler). Generating force field parameters is well beyond the scope of what is or should be included in GROMACS documentation. We provide a few resources in terms of the implementation, but given the vast scope of this topic, and the expert knowledge required, it is impossible to teach people to derive parameters suitably. For that, you need to read and understand the literature regarding the parametrization theory and methods of your chosen force field. At least you've arrived at your answer - you have sub-optimal parameters for 8-oxoG that cause a crash. Now the task is to derive parameters of suitable quality. -- 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] To post
Hi, I would like to post my queries for Gromacs. 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] patched version installation for free energy
Hi Justin, Do you think that there is a bug? If yes, what will we do now? 2015-07-01 19:09 GMT+02:00 Ahmet Yıldırım ahmedo...@gmail.com: :) yes. 2015-07-01 19:08 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 7/1/15 1:05 PM, Ahmet Yıldırım wrote: I am already trying to install it into a separate directory. Source files is in the gromacs-patched folder. I created gromacs directory away from $HOME/Public/gromacs-patched. And you get the same error, even after starting from a fresh build directory? -Justin 2015-07-01 18:56 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 7/1/15 12:52 PM, Ahmet Yıldırım wrote: Hi, When I install the patched GROMACS version ( https://github.com/gromacs/gromacs/tree/022ad08b2fd0c1de085e88ac81a61841c4daea9c ) on cluster, I get the following error after command-2. Why do I get this error? Command-1: t-mn01 [~/Public/gromacs]$ cmake ../gromacs-patched -DGMX_GPU=OFF -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/a/user/Public/gromacs Don't install into the source tree. -Justin -- Configuring done -- Generating done -- Build files have been written to: /home/a/user/Public/gromacs Command-2: t-mn01 [~/Public/gromacs]$ make -j 8 install -- Installing: /home/a/user/Public/gromacs/include/gromacs/trajectoryanalysis/cmdlinerunner.h CMake Error at src/programs/cmake_install.cmake:42 (FILE): file INSTALL cannot find /home/a/user/Public/gromacs/bin/gmx_mpi. Call Stack (most recent call first): src/cmake_install.cmake:40 (INCLUDE) cmake_install.cmake:44 (INCLUDE) make: *** [install] Error 1 -- == 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. -- Ahmet Yıldırım -- Ahmet Yıldırım -- 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] patched version installation for free energy
On 7/1/15 7:00 PM, Ahmet Yıldırım wrote: Hi Justin, Do you think that there is a bug? If yes, what will we do now? Doubtful. I installed that code myself to test it. Of course, I got it directly from the GROMACS repository via Gerrit, but I doubt that makes a difference. I can't explain your observation; the code should install cleanly if done correctly. Maybe someone else has an idea. FWIW, the latest master and release-5-1 branches have the intermolecular bondeds code, so you could try pulling either via git and installing that version. -Justin 2015-07-01 19:09 GMT+02:00 Ahmet Yıldırım ahmedo...@gmail.com: :) yes. 2015-07-01 19:08 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 7/1/15 1:05 PM, Ahmet Yıldırım wrote: I am already trying to install it into a separate directory. Source files is in the gromacs-patched folder. I created gromacs directory away from $HOME/Public/gromacs-patched. And you get the same error, even after starting from a fresh build directory? -Justin 2015-07-01 18:56 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 7/1/15 12:52 PM, Ahmet Yıldırım wrote: Hi, When I install the patched GROMACS version ( https://github.com/gromacs/gromacs/tree/022ad08b2fd0c1de085e88ac81a61841c4daea9c ) on cluster, I get the following error after command-2. Why do I get this error? Command-1: t-mn01 [~/Public/gromacs]$ cmake ../gromacs-patched -DGMX_GPU=OFF -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/a/user/Public/gromacs Don't install into the source tree. -Justin -- Configuring done -- Generating done -- Build files have been written to: /home/a/user/Public/gromacs Command-2: t-mn01 [~/Public/gromacs]$ make -j 8 install -- Installing: /home/a/user/Public/gromacs/include/gromacs/trajectoryanalysis/cmdlinerunner.h CMake Error at src/programs/cmake_install.cmake:42 (FILE): file INSTALL cannot find /home/a/user/Public/gromacs/bin/gmx_mpi. Call Stack (most recent call first): src/cmake_install.cmake:40 (INCLUDE) cmake_install.cmake:44 (INCLUDE) make: *** [install] Error 1 -- == 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. -- Ahmet Yıldırım -- == 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] patched version installation for free energy
Thanks. I think this command git clone git://git.gromacs.org/gromacs.git pulls the latest version? But I need the patched version. How can I pull the patched version ( https://github.com/gromacs/gromacs/tree/022ad08b2fd0c1de085e88ac81a61841c4daea9c) via git? 2015-07-02 1:02 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 7/1/15 7:00 PM, Ahmet Yıldırım wrote: Hi Justin, Do you think that there is a bug? If yes, what will we do now? Doubtful. I installed that code myself to test it. Of course, I got it directly from the GROMACS repository via Gerrit, but I doubt that makes a difference. I can't explain your observation; the code should install cleanly if done correctly. Maybe someone else has an idea. FWIW, the latest master and release-5-1 branches have the intermolecular bondeds code, so you could try pulling either via git and installing that version. -Justin 2015-07-01 19:09 GMT+02:00 Ahmet Yıldırım ahmedo...@gmail.com: :) yes. 2015-07-01 19:08 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 7/1/15 1:05 PM, Ahmet Yıldırım wrote: I am already trying to install it into a separate directory. Source files is in the gromacs-patched folder. I created gromacs directory away from $HOME/Public/gromacs-patched. And you get the same error, even after starting from a fresh build directory? -Justin 2015-07-01 18:56 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 7/1/15 12:52 PM, Ahmet Yıldırım wrote: Hi, When I install the patched GROMACS version ( https://github.com/gromacs/gromacs/tree/022ad08b2fd0c1de085e88ac81a61841c4daea9c ) on cluster, I get the following error after command-2. Why do I get this error? Command-1: t-mn01 [~/Public/gromacs]$ cmake ../gromacs-patched -DGMX_GPU=OFF -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/a/user/Public/gromacs Don't install into the source tree. -Justin -- Configuring done -- Generating done -- Build files have been written to: /home/a/user/Public/gromacs Command-2: t-mn01 [~/Public/gromacs]$ make -j 8 install -- Installing: /home/a/user/Public/gromacs/include/gromacs/trajectoryanalysis/cmdlinerunner.h CMake Error at src/programs/cmake_install.cmake:42 (FILE): file INSTALL cannot find /home/a/user/Public/gromacs/bin/gmx_mpi. Call Stack (most recent call first): src/cmake_install.cmake:40 (INCLUDE) cmake_install.cmake:44 (INCLUDE) make: *** [install] Error 1 -- == 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. -- Ahmet Yıldırım -- == 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. -- Ahmet Yıldırım -- Gromacs Users mailing list * Please search the
Re: [gmx-users] patched version installation for free energy
On 7/1/15 7:39 PM, Ahmet Yıldırım wrote: Thanks. I think this command git clone git://git.gromacs.org/gromacs.git pulls the latest version? But I need the patched version. How can I pull the patched version ( https://github.com/gromacs/gromacs/tree/022ad08b2fd0c1de085e88ac81a61841c4daea9c) via git? As I said, it's already merged. You don't need to patch anything. 1. git clone git://git.gromacs.org/gromacs.git 2. Install the code 3. Profit? -Justin 2015-07-02 1:02 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 7/1/15 7:00 PM, Ahmet Yıldırım wrote: Hi Justin, Do you think that there is a bug? If yes, what will we do now? Doubtful. I installed that code myself to test it. Of course, I got it directly from the GROMACS repository via Gerrit, but I doubt that makes a difference. I can't explain your observation; the code should install cleanly if done correctly. Maybe someone else has an idea. FWIW, the latest master and release-5-1 branches have the intermolecular bondeds code, so you could try pulling either via git and installing that version. -Justin 2015-07-01 19:09 GMT+02:00 Ahmet Yıldırım ahmedo...@gmail.com: :) yes. 2015-07-01 19:08 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 7/1/15 1:05 PM, Ahmet Yıldırım wrote: I am already trying to install it into a separate directory. Source files is in the gromacs-patched folder. I created gromacs directory away from $HOME/Public/gromacs-patched. And you get the same error, even after starting from a fresh build directory? -Justin 2015-07-01 18:56 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 7/1/15 12:52 PM, Ahmet Yıldırım wrote: Hi, When I install the patched GROMACS version ( https://github.com/gromacs/gromacs/tree/022ad08b2fd0c1de085e88ac81a61841c4daea9c ) on cluster, I get the following error after command-2. Why do I get this error? Command-1: t-mn01 [~/Public/gromacs]$ cmake ../gromacs-patched -DGMX_GPU=OFF -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/a/user/Public/gromacs Don't install into the source tree. -Justin -- Configuring done -- Generating done -- Build files have been written to: /home/a/user/Public/gromacs Command-2: t-mn01 [~/Public/gromacs]$ make -j 8 install -- Installing: /home/a/user/Public/gromacs/include/gromacs/trajectoryanalysis/cmdlinerunner.h CMake Error at src/programs/cmake_install.cmake:42 (FILE): file INSTALL cannot find /home/a/user/Public/gromacs/bin/gmx_mpi. Call Stack (most recent call first): src/cmake_install.cmake:40 (INCLUDE) cmake_install.cmake:44 (INCLUDE) make: *** [install] Error 1 -- == 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. -- Ahmet Yıldırım -- == 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
[gmx-users] Gromacs MD application expert position in Stockholm
Hi, Normally we’re somewhat restrictive with allowing general announcements for positions on this list, but this particular position will be heavily focused on developing Gromacs itself together with the Stockholm team. The national supercomputing center PDC in Stockholm is one of our closest partners, and we are looking to hire 1-2 outstanding MD experts and programmers. You will spend part of your time at the supercomputing center, and part of your time in the Gromacs team. Experience with GPU programming would be a strong merit. Note that you have to apply through KTH’s recruitment systems (no mails, in particular not to me). The job will require full time physical presence in Stockholm. https://www.kth.se/en/om/work-at-kth/lediga-jobb/what:job/jobID:70101/where:4/ Cheers, Erik -- Erik Lindahl erik.lind...@gmail.com Professor of Biophysics, Dept. Biochemistry Biophysics, Stockholm University Professor of Theoretical biophysics, Dept. Theoretical Physics, Royal Inst. Technology Science for Life Laboratory, Box 1031, 17121 Solna, Sweden -- 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] GPU and aux power supply
Hmmm, 8x sounds rather high, are you sure you are comparing to CPU-only runs that use proper SIMD optimized kernels? Because of the way offload-based acceleration works, the CPU and GPU will inherently be executing concurrently only part of the runtime and as a consequence the GPU is idle part of the run-time (during integration+constraints). You can make use of this idle time by running multiple independent simulations concurrently. This can yield serious improvements in terms of _aggregate_ simulation performance especially with small inputs and many cores (see slide 51 https://goo.gl/7DnSri)/ -- Szilárd On Wed, Jul 1, 2015 at 4:16 AM, Alex nedoma...@gmail.com wrote: I am happy to say that I am getting an 8-fold increase in simulation speeds for $200. An additional question: normally, how many simulations (separate mdruns on separate CPU cores) can be performed simultaneously on a single GPU? Say, for 20-40K particle sized simulations. The coolers are not even spinning during a single test (mdrun -ntomp 4), and I get massive acceleration. They aren't broken, the card is just cool (small system, ~3K particles). Thanks, Alex Ah, ok, so you can get a 6-pin from the PSU and another from a converted molex connector. That should be just fine, especially as the card should will not pull more than ~155W (under heavy graphics load) based on the Tomshardware review* and you are providing 225W max. * http://www.tomshardware.com/reviews/evga-super-super-clocked-gtx-960,4063-3.html -- Szilárd On Tue, Jun 30, 2015 at 7:31 PM, Alex nedoma...@gmail.com wrote: Well, I don't have one like this. What I have instead is this: 1. A single 6-pin directly from the PSU. 2. A single molex to 6-pin (my PSU does provide one molex). 3. Two 6-pins to a single 8-pin converter going to the card. In other words, I can populate both 6-pins on the 6-8 converter, just not sure about the pinouts in this case. Not good? Alex What I meant is this: http://goo.gl/8o1B5P That is 2x molex - 8pin PCI-E. A single molex may not be enouhg. -- Szilárd On Tue, Jun 30, 2015 at 7:10 PM, Alex nedoma...@gmail.com wrote: It is a 4-core CPU, single GPU box, so I doubt I will be running more than one at a time. We will very likely get a different PSU, unless... I do have a molex to 6 pin concerter sitting on this very desk. Do you think it will satisfy the card? I just don't know how much a single molex line delivers. If you feel this should work, off to installing everything I go. Thanks a bunch, Alex SP First of all, unless you run multiple independent simulations on the same SP GPU, GROMACS runs alone will never get anywhere near the peak power SP consumption of the GPU. SP The good news is that NVIDIA has gained some sanity and stopped blocking SP GeForce GPU info in nvidia-smi - although only for newer cars, but it does SP work with the 960 if you use a 352.xx driver: SP +--+ SP | NVIDIA-SMI 352.21 Driver Version: 352.21 | SP |---+--+--+ SP | GPU NamePersistence-M| Bus-IdDisp.A | Volatile Uncorr. SP ECC | SP | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute SP M. | SP |===+==+==| SP | 0 GeForce GTX 960 Off | :01:00.0 On | SP N/A | SP | 8% 45CP515W / 130W | 1168MiB / 2044MiB | 31% SP Default | SP +---+--+--+ SP A single 6-pin can deliver 75W, an 8-pin 150W, so in your case, the hard SP limits of what your card can pull is 75W from the PCI-E slow + 150W from SP the cable = 225 W. With a single 6-pin cable you'll only get ~150W max. SP That can be OK if your card does not pull more power (e.g. the above SP non-overclocked card would be just fine), but as your card is overclocked, SP I'm not sure it won't peak above 150W. SP You can try to get a molex - PCI-E power cable converter. SP -- SP Szilárd SP On Mon, Jun 29, 2015 at 9:56 PM, Alex nedoma...@gmail.com wrote: Hi all, I have a bit of a gromacs-unrelated question here, but I think this is a better place to ask it than, say, a gaming forum. The Nvidia GTX 960 card we got here came with an 8-pin AUX connector on the card side, which interfaces _two_ 6-pin connectors to the PSU. It is a factory superclocked card. My 525W PSU can only populate _one_ of those 6-pin connectors. The EVGA website states that I need at least 400W PSU, while I have 525. At the same time, I have a dedicated high-power PCI-e slot, which on the motherboard says 75W PCI-e. Do I need a different PSU to populate the AUX power connector completely? Are these runs
Re: [gmx-users] GPU and aux power supply
Yup, about 7-8 times between with and without GPU acceleration, not making this up: I had 11 ns/day and now ~80-87 ns/day, the numbers vary a bit. I've been getting a similar boost on our GPU-accelerated cluster node (dual core i7, 8 cores each) with two Tesla C2075 cards (I am directing my simulations to one of them via -gpu_id). All runs are -ntomp 4, with or without GPU. The physics in all cases is perfectly acceptable. So far I only tested my new box on vacuum simulations, about to run the solvated version (~30K particles). Alex On Wed, Jul 1, 2015 at 6:09 PM, Szilárd Páll pall.szil...@gmail.com wrote: Hmmm, 8x sounds rather high, are you sure you are comparing to CPU-only runs that use proper SIMD optimized kernels? Because of the way offload-based acceleration works, the CPU and GPU will inherently be executing concurrently only part of the runtime and as a consequence the GPU is idle part of the run-time (during integration+constraints). You can make use of this idle time by running multiple independent simulations concurrently. This can yield serious improvements in terms of _aggregate_ simulation performance especially with small inputs and many cores (see slide 51 https://goo.gl/7DnSri)/ -- Szilárd On Wed, Jul 1, 2015 at 4:16 AM, Alex nedoma...@gmail.com wrote: I am happy to say that I am getting an 8-fold increase in simulation speeds for $200. An additional question: normally, how many simulations (separate mdruns on separate CPU cores) can be performed simultaneously on a single GPU? Say, for 20-40K particle sized simulations. The coolers are not even spinning during a single test (mdrun -ntomp 4), and I get massive acceleration. They aren't broken, the card is just cool (small system, ~3K particles). Thanks, Alex Ah, ok, so you can get a 6-pin from the PSU and another from a converted molex connector. That should be just fine, especially as the card should will not pull more than ~155W (under heavy graphics load) based on the Tomshardware review* and you are providing 225W max. * http://www.tomshardware.com/reviews/evga-super-super-clocked-gtx-960,4063-3.html -- Szilárd On Tue, Jun 30, 2015 at 7:31 PM, Alex nedoma...@gmail.com wrote: Well, I don't have one like this. What I have instead is this: 1. A single 6-pin directly from the PSU. 2. A single molex to 6-pin (my PSU does provide one molex). 3. Two 6-pins to a single 8-pin converter going to the card. In other words, I can populate both 6-pins on the 6-8 converter, just not sure about the pinouts in this case. Not good? Alex What I meant is this: http://goo.gl/8o1B5P That is 2x molex - 8pin PCI-E. A single molex may not be enouhg. -- Szilárd On Tue, Jun 30, 2015 at 7:10 PM, Alex nedoma...@gmail.com wrote: It is a 4-core CPU, single GPU box, so I doubt I will be running more than one at a time. We will very likely get a different PSU, unless... I do have a molex to 6 pin concerter sitting on this very desk. Do you think it will satisfy the card? I just don't know how much a single molex line delivers. If you feel this should work, off to installing everything I go. Thanks a bunch, Alex SP First of all, unless you run multiple independent simulations on the same SP GPU, GROMACS runs alone will never get anywhere near the peak power SP consumption of the GPU. SP The good news is that NVIDIA has gained some sanity and stopped blocking SP GeForce GPU info in nvidia-smi - although only for newer cars, but it does SP work with the 960 if you use a 352.xx driver: SP +--+ SP | NVIDIA-SMI 352.21 Driver Version: 352.21 | SP |---+--+--+ SP | GPU NamePersistence-M| Bus-IdDisp.A | Volatile Uncorr. SP ECC | SP | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute SP M. | SP |===+==+==| SP | 0 GeForce GTX 960 Off | :01:00.0 On | SP N/A | SP | 8% 45CP515W / 130W | 1168MiB / 2044MiB | 31% SP Default | SP +---+--+--+ SP A single 6-pin can deliver 75W, an 8-pin 150W, so in your case, the hard SP limits of what your card can pull is 75W from the PCI-E slow + 150W from SP the cable = 225 W. With a single 6-pin cable you'll only get ~150W max. SP That can be OK if your card does not pull more power (e.g. the above SP non-overclocked card would be just fine), but as your card is overclocked, SP I'm not sure it won't peak above 150W. SP You can try to get a molex - PCI-E power cable converter. SP -- SP Szilárd SP On Mon, Jun 29, 2015 at 9:56 PM, Alex nedoma...@gmail.com wrote: Hi all, I have a bit of a
