Re: [gmx-users] help about ibi
Hi, Something went wrong earlier in your workflow. Check your log files, etc. Mark On Nov 13, 2013 3:57 AM, guozhicheng222 guozhicheng...@126.com wrote: Hi: When I am running the ibi procedure, I get the following error message: A coordinate in file conf.gro does not contain a '.' Additionally, I check the coordinate file of confout.gro in step_001. It showed that 'nan' symbol appeared in confout.gro. What is wrong with this? How can I fix it? I am very appreciating for anyone's help. Best Wishes! Zhicheng Guo -- 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] help about ibi
Hi: When I am running the ibi procedure, I get the following error message: A coordinate in file conf.gro does not contain a '.' Additionally, I check the coordinate file of confout.gro in step_001. It showed that 'nan' symbol appeared in confout.gro. What is wrong with this? How can I fix it? I am very appreciating for anyone's help. Best Wishes! Zhicheng Guo-- 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] help about logfile
Hi I am confusing with the output file (.log) about the sample frequency (frames) in my simulation. The average information in .log file is 'Statistics over 31 steps using 3001 frames' where nstxout =4000 and nstlog =4000. While, 'Statistics over 31 steps using 20001 frames', appeared in .log file, where nstxout =15 and nstlog =15. In my opinion, the former sample frequency should be 75 frames rather than 3001 frames and the latter is right. I want to know how can I control the sample frequency, arbitrarily.-- 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] help about logfile
On 11/11/13 5:04 AM, guozhicheng222 wrote: Hi I am confusing with the output file (.log) about the sample frequency (frames) in my simulation. The average information in .log file is 'Statistics over 31 steps using 3001 frames' where nstxout =4000 and nstlog =4000. While, 'Statistics over 31 steps using 20001 frames', appeared in .log file, where nstxout =15 and nstlog =15. In my opinion, the former sample frequency should be 75 frames rather than 3001 frames and the latter is right. I want to know how can I control the sample frequency, arbitrarily. Check to make sure you set nstlog correctly in the first run. Look for the value in the .log file itself. It is highly unlikely that something so fundamental and simple is being executed incorrectly in one run, but correctly in another. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Help to simulate gas mixture
Dear Friends, I am just a beginner in using GROMCS-4.6.3 and I want to simulate gas mixture, the same as mixture of O2 and N2, any help(the same as introducing a reference, not GROMACS manual b/c there is no explanation about gas mixture) is appreciated. Kind Regards, Ali -- View this message in context: http://gromacs.5086.x6.nabble.com/Help-to-simulate-gas-mixture-tp5012193.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] Help to simulate gas mixture
The principle is the same as at http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents On Nov 3, 2013 6:55 PM, ali.nazari ali.nazari.a...@gmail.com wrote: Dear Friends, I am just a beginner in using GROMCS-4.6.3 and I want to simulate gas mixture, the same as mixture of O2 and N2, any help(the same as introducing a reference, not GROMACS manual b/c there is no explanation about gas mixture) is appreciated. Kind Regards, Ali -- View this message in context: http://gromacs.5086.x6.nabble.com/Help-to-simulate-gas-mixture-tp5012193.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 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] Help g_energy
Hello. I was calculating the viscosity of hexane through the Gromacs command g_energy. Three files are generated: visco.xvg, evisco.xvg and eviscoi.xvg. The file visco.xvg presents the shear viscosity and bulk, but the value does not match the experimental. I used 8 ns simulation at equilibrium. However, the file evisco.xvg has a value very close to the experimental but has only a time of 2 ns (version 4.0.7). I want to know what is present in the file eviscoi.xvg. Thank you. http://help-gromacs.blogspot.com.br/2013/09/viscosidade-gromacs-407.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
[gmx-users] Help g_energy
Hello. I was calculating the viscosity of hexane through the Gromacs command g_energy. Three files are generated: visco.xvg, evisco.xvg and eviscoi.xvg. The file visco.xvg presents the shear viscosity and bulk, but the value does not match the experimental. I used 8 ns simulation at equilibrium. However, the file evisco.xvg has a value very close to the experimental but has only a time of 2 ns (version 4.0.7). I want to know what is present in the file eviscoi.xvg. Thank you. http://help-gromacs.blogspot.com.br/2013/09/viscosidade-gromacs-407.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
[gmx-users] Help on itp and pdb
If I use the topology and coordinates of a small molecule from ATB for docking (structure.pdb / structure.itp which match in atom numbering and sequence); after docking and saving the structure_dock.pdb, the atom numbering does not match the numbering in the structure.itp file. This causes errors during simulation. How to regular the numbering so that it matches the structure.itp file from ATB Please help Regards -Original Message- From: gmx-users-requ...@gromacs.org Sent: Friday, September 06, 2013 3:30 PM To: gmx-users@gromacs.org Subject: gmx-users Digest, Vol 113, Issue 23 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: Segmentation Fault using g_cluster (deplazes) 2. Re: Re: Segmentation Fault using g_cluster (Tsjerk Wassenaar) 3. Re: Segmentation Fault using g_cluster (deplazes) -- Message: 1 Date: Thu, 5 Sep 2013 22:20:16 -0700 (PDT) From: deplazes e.depla...@uq.edu.au Subject: [gmx-users] Re: Segmentation Fault using g_cluster To: gmx-users@gromacs.org Message-ID: 1378444816131-5011007.p...@n6.nabble.com Content-Type: text/plain; charset=us-ascii Hi guys do you have an idea what is causing the segmentation fault with g_cluster? I do the following 1 . I combine trr files from different simulations using trjcat and select backbone atoms only trjcat -f ../../*C/runs/*/*trr -cat -n index.ndx -o trajout_combined.xtc 2. I make a new .tpr file for the backbone atoms only tpbconv -s run_1.tpr -nsteps -1 -n index.ndx -o topol.tpr 3. I run g_cluster on the combined trajout with the new tpr selecting backbone for RMSD fit and output g_cluster -f trajout_combined.xtc -n index.ndx -s topol.tpr -fit -method gromos -sz clust-size_0.20.xvg -o rmsd-clust_0.20.xpm -g cluster_0.20.log -clid clust-id_0.20.xvg -cl clusters_0.20.pdb -dist rmsd-dist_0.20.xvg -cutoff 0.20 the output is Allocated 12066120 bytes for frames Read 1202 frames from trajectory trajout_combined.xtc Computing 1202x1202 RMS deviation matrix # RMSD calculations left: 0 The RMSD ranges from 0.0601062 to 0.533457 nm Average RMSD is 0.321503 Number of structures for matrix 1202 Energy of the matrix is 160.564 nm WARNING: rmsd minimum 0 is below lowest rmsd value 0.0601062 Making list of neighbors within cutoff 100% Finding clusters7 Found 7 clusters Writing middle structure for each cluster to clusters_0.20.pdb Segmentation fault I have tried using less frames (using -dt 500 for trjcat) as to check that it is not a memory issue but still get the seg fault The g_cluster works if I use a trajectory from a single simulations but not for hte combined trajout. I am getting a segmentation fault with both gromacs 4.5.5 (on my macbook pro) and 4.6.3 on raijin.nci.org.au (our supercomputing facilities in Australia) Cheers Evelyne -- View this message in context: http://gromacs.5086.x6.nabble.com/Segmentation-Fault-using-g-cluster-tp4662864p5011007.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Message: 2 Date: Fri, 6 Sep 2013 11:10:49 +0200 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] Re: Segmentation Fault using g_cluster To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: cabze1sjhuc9bxcybcrdkeav7bbvbujggcrhvdmvzh7-sghd...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hi Evelyne, I haven't got a clue... But does it work if you use -settime when concatenating the trajectories, to avoid having frames with the same time index? It shouldn't cause a segfault, but it might. Cheers, Tsjerk On Fri, Sep 6, 2013 at 7:20 AM, deplazes e.depla...@uq.edu.au wrote: Hi guys do you have an idea what is causing the segmentation fault with g_cluster? I do the following 1 . I combine trr files from different simulations using trjcat and select backbone atoms only trjcat -f ../../*C/runs/*/*trr -cat -n index.ndx -o trajout_combined.xtc 2. I make a new .tpr file for the backbone atoms only tpbconv -s run_1.tpr -nsteps -1 -n index.ndx -o topol.tpr 3. I run g_cluster on the combined trajout with the new tpr selecting backbone for RMSD fit and output g_cluster -f trajout_combined.xtc -n index.ndx -s topol.tpr -fit -method gromos -sz clust-size_0.20.xvg -o rmsd-clust_0.20.xpm -g cluster_0.20.log -clid clust-id_0.20.xvg -cl clusters_0.20.pdb -dist rmsd-dist_0.20.xvg -cutoff 0.20 the output is Allocated 12066120 bytes for frames Read 1202 frames from trajectory trajout_combined.xtc Computing 1202x1202 RMS
Re: [gmx-users] Help on itp and pdb
Please don't reply to the entire digest; the archive is hopelessly confused as it is, but let's not make it any worse ;) On 9/6/13 2:29 PM, R R S Pissurlenkar wrote: If I use the topology and coordinates of a small molecule from ATB for docking (structure.pdb / structure.itp which match in atom numbering and sequence); after docking and saving the structure_dock.pdb, the atom numbering does not match the numbering in the structure.itp file. This causes errors during simulation. How to regular the numbering so that it matches the structure.itp file from ATB The numbering of the atoms in the coordinate file should have no relevance on the .itp file, which must be numbered from 1. If atoms in the coordinate file are out of order with respect to the topology, there's no real choice but to reorder them manually in a text editor, but that's only something you should ever have to do once. If you need more explicit advice, please provide exact input, output, and any relevant error messages (copied and pasted from the terminal, please). -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] help
I am facing a problem while simulating the tRNA molecule while converting pdb to gro, Fatal error: Atom OP3 in residue A 1 was not found in rtp entry RA5 with 31 atoms while sorting atoms. force field used 3 (AMBER96 protein, nucleic AMBER94), water model TIP3P. i checked in gromacs error list, in that they mentioned simply re-name the atoms in your coordinate filehttp://www.gromacs.org/Documentation/File_Formats/Coordinate_File , how to rename the atom in coordinate file kindly give valuable suggestion how to rectify this error, Awaiting For your reply Thanking 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] help
On 9/4/13 6:04 AM, Prajisha Sujaya wrote: I am facing a problem while simulating the tRNA molecule while converting pdb to gro, Fatal error: Atom OP3 in residue A 1 was not found in rtp entry RA5 with 31 atoms while sorting atoms. force field used 3 (AMBER96 protein, nucleic AMBER94), water model TIP3P. i checked in gromacs error list, in that they mentioned simply re-name the atoms in your coordinate filehttp://www.gromacs.org/Documentation/File_Formats/Coordinate_File , how to rename the atom in coordinate file Use a text editor. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Help with Error Message
Hey :) Sorry for replying a bit late. But the issues you mention in this and the other posts are usually solved by closely reading the text of the tutorial, not only the commands. Cheers, Tsjerk On Sun, Aug 25, 2013 at 3:44 AM, The One And Only chappybo...@gmail.comwrote: Never mind, I'm dumb. I just realized that protein.pdb means i have to specify which protein i want like 1qlz.pdb and not actually type protein.pdb BUT THANKS GUYS!! On Sat, Aug 24, 2013 at 6:40 PM, The One And Only chappybo...@gmail.com wrote: so how do i solve the protein.pdb issue? On Sat, Aug 24, 2013 at 6:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/24/13 9:26 PM, The One And Only wrote: that's something i know nothing about; I just graduated from high school and I have no background or experience in open source projects or programs like pymol/gromacs. My professor wants me to be able to produce a setup, simulation, and analysis within a week so I'm pretty desperate right now in terms of getting help. Do you know how to get the right .pdb file in my working directory? Rudimentary Unix commands like cp and mv are covered in any Unix/Linux tutorial. Google can find lots of good ones. Producing a quality simulation cannot be rushed, and if you don't know the fundamentals of navigating the command line and directory structure, it's nearly impossible. You need to invest time in learning the environment before doing anything, I'm afraid. Just to give a bit of perspective, we used to train our undergrads for nearly a full semester (at least 2-3 months) before requiring them to do any real work. At least a week or two of that time was spent getting used to command line and Linux in general. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 ==** -- 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 -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Help with Error Message
I've moved on from that point; now I'm stuck at where it asks me to remove molecules of solvent from the topology file. On Tue, Aug 27, 2013 at 1:33 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hey :) Sorry for replying a bit late. But the issues you mention in this and the other posts are usually solved by closely reading the text of the tutorial, not only the commands. Cheers, Tsjerk On Sun, Aug 25, 2013 at 3:44 AM, The One And Only chappybo...@gmail.com wrote: Never mind, I'm dumb. I just realized that protein.pdb means i have to specify which protein i want like 1qlz.pdb and not actually type protein.pdb BUT THANKS GUYS!! On Sat, Aug 24, 2013 at 6:40 PM, The One And Only chappybo...@gmail.com wrote: so how do i solve the protein.pdb issue? On Sat, Aug 24, 2013 at 6:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/24/13 9:26 PM, The One And Only wrote: that's something i know nothing about; I just graduated from high school and I have no background or experience in open source projects or programs like pymol/gromacs. My professor wants me to be able to produce a setup, simulation, and analysis within a week so I'm pretty desperate right now in terms of getting help. Do you know how to get the right .pdb file in my working directory? Rudimentary Unix commands like cp and mv are covered in any Unix/Linux tutorial. Google can find lots of good ones. Producing a quality simulation cannot be rushed, and if you don't know the fundamentals of navigating the command line and directory structure, it's nearly impossible. You need to invest time in learning the environment before doing anything, I'm afraid. Just to give a bit of perspective, we used to train our undergrads for nearly a full semester (at least 2-3 months) before requiring them to do any real work. At least a week or two of that time was spent getting used to command line and Linux in general. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 ==** -- 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 -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] Help with Error Message
Hi ..., You should have had a look at the topology file format in an earlier step. At the end is a listing of molecules. As it says in the tutorial, you replaced solvent by ions, and you have to make changes in the topology file to match that replacement. Open the file in an editor, have a look around, try to see where the number of solvent molecules is listed, and make the changes. Cheers, Tsjerk On Tue, Aug 27, 2013 at 10:41 PM, The One And Only chappybo...@gmail.comwrote: I've moved on from that point; now I'm stuck at where it asks me to remove molecules of solvent from the topology file. On Tue, Aug 27, 2013 at 1:33 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hey :) Sorry for replying a bit late. But the issues you mention in this and the other posts are usually solved by closely reading the text of the tutorial, not only the commands. Cheers, Tsjerk On Sun, Aug 25, 2013 at 3:44 AM, The One And Only chappybo...@gmail.com wrote: Never mind, I'm dumb. I just realized that protein.pdb means i have to specify which protein i want like 1qlz.pdb and not actually type protein.pdb BUT THANKS GUYS!! On Sat, Aug 24, 2013 at 6:40 PM, The One And Only chappybo...@gmail.com wrote: so how do i solve the protein.pdb issue? On Sat, Aug 24, 2013 at 6:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/24/13 9:26 PM, The One And Only wrote: that's something i know nothing about; I just graduated from high school and I have no background or experience in open source projects or programs like pymol/gromacs. My professor wants me to be able to produce a setup, simulation, and analysis within a week so I'm pretty desperate right now in terms of getting help. Do you know how to get the right .pdb file in my working directory? Rudimentary Unix commands like cp and mv are covered in any Unix/Linux tutorial. Google can find lots of good ones. Producing a quality simulation cannot be rushed, and if you don't know the fundamentals of navigating the command line and directory structure, it's nearly impossible. You need to invest time in learning the environment before doing anything, I'm afraid. Just to give a bit of perspective, we used to train our undergrads for nearly a full semester (at least 2-3 months) before requiring them to do any real work. At least a week or two of that time was spent getting used to command line and Linux in general. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 ==** -- 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 -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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 -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing list
Re: [gmx-users] Help with Error Message
What kind of editor should I open it in? I have Pymol, but I don't know if it's the right one. -- 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] Help with Error Message
a text editor On Tue, Aug 27, 2013 at 1:54 PM, The One And Only chappybo...@gmail.comwrote: What kind of editor should I open it in? I have Pymol, but I don't know if it's the right one. -- 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] Help with Error Message
An editor is a program to edit the text in a file: gedit, nano, vi, emacs, ... It'll be the equivalent of Windows' Notepad. Can you find a tutor around to help you out with the basic usage of Linux? It's always difficult to plunge into several different things at the same time, here 'using linux', 'performing simulations', and probably 'theory of molecular dynamics'. It helps to take one topic at a time, but that is not always possible. Cheers, T. On Tue, Aug 27, 2013 at 10:56 PM, Rafael I. Silverman y de la Vega rsilv...@ucsc.edu wrote: a text editor On Tue, Aug 27, 2013 at 1:54 PM, The One And Only chappybo...@gmail.com wrote: What kind of editor should I open it in? I have Pymol, but I don't know if it's the right one. -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Help with Error Message
So I started following some tutorials online since I didn't get a response last time. the tutorial I'm using is: http://nmr.chem.uu.nl/%7Etsjerk/course/molmod/ I followed that tutorial to the second page and got stuck at the step where it asks you to input: pdb2gmx -f protein.pdb -o protein.gro -p protein.top -ignh I picked GROMOS96 45a3 force field(11) for the force field and spc(1) for the water model but got the following error message: Opening force field file /usr/local/gromacs/share/gromacs/top/gromos45a3.ff/aminoacids.r2b Reading protein.pdb... --- Program pdb2gmx, VERSION 4.6.3 Source code file: /Users/christinalin/wget-1.14/gromacs-4.6.3/src/gmxlib/futil.c, line: 593 File input/output error: protein.pdb For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Help please? -- 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] Help with Error Message
It sounds like you dont have the .pdb file in your working directory. Perhaps you need to learn a bit about unix filesystems On Sat, Aug 24, 2013 at 6:18 PM, The One And Only chappybo...@gmail.comwrote: So I started following some tutorials online since I didn't get a response last time. the tutorial I'm using is: http://nmr.chem.uu.nl/%7Etsjerk/course/molmod/ I followed that tutorial to the second page and got stuck at the step where it asks you to input: pdb2gmx -f protein.pdb -o protein.gro -p protein.top -ignh I picked GROMOS96 45a3 force field(11) for the force field and spc(1) for the water model but got the following error message: Opening force field file /usr/local/gromacs/share/gromacs/top/gromos45a3.ff/aminoacids.r2b Reading protein.pdb... --- Program pdb2gmx, VERSION 4.6.3 Source code file: /Users/christinalin/wget-1.14/gromacs-4.6.3/src/gmxlib/futil.c, line: 593 File input/output error: protein.pdb For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Help please? -- 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] Help with Error Message
that's something i know nothing about; I just graduated from high school and I have no background or experience in open source projects or programs like pymol/gromacs. My professor wants me to be able to produce a setup, simulation, and analysis within a week so I'm pretty desperate right now in terms of getting help. Do you know how to get the right .pdb file in my working directory? On Sat, Aug 24, 2013 at 6:23 PM, Rafael I. Silverman y de la Vega rsilv...@ucsc.edu wrote: It sounds like you dont have the .pdb file in your working directory. Perhaps you need to learn a bit about unix filesystems On Sat, Aug 24, 2013 at 6:18 PM, The One And Only chappybo...@gmail.com wrote: So I started following some tutorials online since I didn't get a response last time. the tutorial I'm using is: http://nmr.chem.uu.nl/%7Etsjerk/course/molmod/ I followed that tutorial to the second page and got stuck at the step where it asks you to input: pdb2gmx -f protein.pdb -o protein.gro -p protein.top -ignh I picked GROMOS96 45a3 force field(11) for the force field and spc(1) for the water model but got the following error message: Opening force field file /usr/local/gromacs/share/gromacs/top/gromos45a3.ff/aminoacids.r2b Reading protein.pdb... --- Program pdb2gmx, VERSION 4.6.3 Source code file: /Users/christinalin/wget-1.14/gromacs-4.6.3/src/gmxlib/futil.c, line: 593 File input/output error: protein.pdb For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Help please? -- 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
Re: [gmx-users] Help with Error Message
On 8/24/13 9:26 PM, The One And Only wrote: that's something i know nothing about; I just graduated from high school and I have no background or experience in open source projects or programs like pymol/gromacs. My professor wants me to be able to produce a setup, simulation, and analysis within a week so I'm pretty desperate right now in terms of getting help. Do you know how to get the right .pdb file in my working directory? Rudimentary Unix commands like cp and mv are covered in any Unix/Linux tutorial. Google can find lots of good ones. Producing a quality simulation cannot be rushed, and if you don't know the fundamentals of navigating the command line and directory structure, it's nearly impossible. You need to invest time in learning the environment before doing anything, I'm afraid. Just to give a bit of perspective, we used to train our undergrads for nearly a full semester (at least 2-3 months) before requiring them to do any real work. At least a week or two of that time was spent getting used to command line and Linux in general. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Help with Error Message
so how do i solve the protein.pdb issue? On Sat, Aug 24, 2013 at 6:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/24/13 9:26 PM, The One And Only wrote: that's something i know nothing about; I just graduated from high school and I have no background or experience in open source projects or programs like pymol/gromacs. My professor wants me to be able to produce a setup, simulation, and analysis within a week so I'm pretty desperate right now in terms of getting help. Do you know how to get the right .pdb file in my working directory? Rudimentary Unix commands like cp and mv are covered in any Unix/Linux tutorial. Google can find lots of good ones. Producing a quality simulation cannot be rushed, and if you don't know the fundamentals of navigating the command line and directory structure, it's nearly impossible. You need to invest time in learning the environment before doing anything, I'm afraid. Just to give a bit of perspective, we used to train our undergrads for nearly a full semester (at least 2-3 months) before requiring them to do any real work. At least a week or two of that time was spent getting used to command line and Linux in general. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Help with Error Message
Never mind, I'm dumb. I just realized that protein.pdb means i have to specify which protein i want like 1qlz.pdb and not actually type protein.pdb BUT THANKS GUYS!! On Sat, Aug 24, 2013 at 6:40 PM, The One And Only chappybo...@gmail.comwrote: so how do i solve the protein.pdb issue? On Sat, Aug 24, 2013 at 6:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/24/13 9:26 PM, The One And Only wrote: that's something i know nothing about; I just graduated from high school and I have no background or experience in open source projects or programs like pymol/gromacs. My professor wants me to be able to produce a setup, simulation, and analysis within a week so I'm pretty desperate right now in terms of getting help. Do you know how to get the right .pdb file in my working directory? Rudimentary Unix commands like cp and mv are covered in any Unix/Linux tutorial. Google can find lots of good ones. Producing a quality simulation cannot be rushed, and if you don't know the fundamentals of navigating the command line and directory structure, it's nearly impossible. You need to invest time in learning the environment before doing anything, I'm afraid. Just to give a bit of perspective, we used to train our undergrads for nearly a full semester (at least 2-3 months) before requiring them to do any real work. At least a week or two of that time was spent getting used to command line and Linux in general. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Help needed in installation
Hi everyone, I am trying to install Gromacs on OS X and following the installation guide, in section 4.1, I get an output shown as follows: Sonikas-MacBook-Pro:Downloads sonikagahlawat$ cd gromacs-4.6.2 Sonikas-MacBook-Pro:gromacs-4.6.2 sonikagahlawat$ cmake cmake version 2.8.11.1 Usage cmake [options] path-to-source cmake [options] path-to-existing-build Options -C initial-cache = Pre-load a script to populate the cache. -D var:type=value = Create a cmake cache entry. -U globbing_expr = Remove matching entries from CMake cache. -G generator-name = Specify a makefile generator. -T toolset-name = Specify toolset name if supported by generator. -Wno-dev= Suppress developer warnings. -Wdev = Enable developer warnings. -E = CMake command mode. -i = Run in wizard mode. -L[A][H]= List non-advanced cached variables. --build dir = Build a CMake-generated project binary tree. -N = View mode only. -P file = Process script mode. --find-package = Run in pkg-config like mode. --graphviz=[file] = Generate graphviz of dependencies. --system-information [file] = Dump information about this system. --debug-trycompile = Do not delete the try_compile build tree. Only useful on one try_compile at a time. --debug-output = Put cmake in a debug mode. --trace = Put cmake in trace mode. --warn-uninitialized= Warn about uninitialized values. --warn-unused-vars = Warn about unused variables. --no-warn-unused-cli= Don't warn about command line options. --check-system-vars = Find problems with variable usage in system files. --help-command cmd [file] = Print help for a single command and exit. --help-command-list [file] = List available listfile commands and exit. --help-commands [file] = Print help for all commands and exit. --help-compatcommands [file]= Print help for compatibility commands. --help-module module [file] = Print help for a single module and exit. --help-module-list [file] = List available modules and exit. --help-modules [file] = Print help for all modules and exit. --help-custom-modules [file]= Print help for all custom modules and exit. --help-policy cmp [file]= Print help for a single policy and exit. --help-policies [file] = Print help for all policies and exit. --help-property prop [file] = Print help for a single property and exit. --help-property-list [file] = List available properties and exit. --help-properties [file]= Print help for all properties and exit. --help-variable var [file] = Print help for a single variable and exit. --help-variable-list [file] = List documented variables and exit. --help-variables [file] = Print help for all variables and exit. --copyright [file] = Print the CMake copyright and exit. --help,-help,-usage,-h,-H,/?= Print usage information and exit. --help-full [file] = Print full help and exit. --help-html [file] = Print full help in HTML format. --help-man [file] = Print full help as a UNIX man page and exit. --version,-version,/V [file]= Show program name/version banner and exit. Generators The following generators are available on this platform: Unix Makefiles = Generates standard UNIX makefiles. Ninja = Generates build.ninja files (experimental). Xcode = Generate Xcode project files. CodeBlocks - Ninja = Generates CodeBlocks project files. CodeBlocks - Unix Makefiles = Generates CodeBlocks project files. Eclipse CDT4 - Ninja= Generates Eclipse CDT 4.0 project files. Eclipse CDT4 - Unix Makefiles = Generates Eclipse CDT 4.0 project files. KDevelop3 = Generates KDevelop 3 project files. KDevelop3 - Unix Makefiles = Generates KDevelop 3 project files. Sublime Text 2 - Ninja = Generates Sublime Text 2 project files. Sublime Text 2 - Unix Makefiles = Generates Sublime Text 2 project files. Sonikas-MacBook-Pro:gromacs-4.6.2 sonikagahlawat$ ccmake ccmake version 2.8.11.1 Usage ccmake path-to-source ccmake path-to-existing-build Options -C initial-cache = Pre-load a script to populate the cache. -D var:type=value = Create a cmake cache entry. -U globbing_expr = Remove matching entries from CMake cache. -G generator-name = Specify a makefile generator. -T toolset-name = Specify toolset name if supported by generator. -Wno-dev= Suppress
Re: [gmx-users] Help needed in installation
Hi Sonika, cmake needs a specification of the path where the source code is. In addition to that, it is best to build it in a separate directory. As explained on the website, in your gromacs directory: mkdir build cd build cmake ../ make make install Hope it helps, Tsjerk On Tue, Jul 2, 2013 at 8:51 PM, Sonika Gahlawat sonika.gahla...@gmail.comwrote: Hi everyone, I am trying to install Gromacs on OS X and following the installation guide, in section 4.1, I get an output shown as follows: Sonikas-MacBook-Pro:Downloads sonikagahlawat$ cd gromacs-4.6.2 Sonikas-MacBook-Pro:gromacs-4.6.2 sonikagahlawat$ cmake cmake version 2.8.11.1 Usage cmake [options] path-to-source cmake [options] path-to-existing-build Options -C initial-cache = Pre-load a script to populate the cache. -D var:type=value = Create a cmake cache entry. -U globbing_expr = Remove matching entries from CMake cache. -G generator-name = Specify a makefile generator. -T toolset-name = Specify toolset name if supported by generator. -Wno-dev= Suppress developer warnings. -Wdev = Enable developer warnings. -E = CMake command mode. -i = Run in wizard mode. -L[A][H]= List non-advanced cached variables. --build dir = Build a CMake-generated project binary tree. -N = View mode only. -P file = Process script mode. --find-package = Run in pkg-config like mode. --graphviz=[file] = Generate graphviz of dependencies. --system-information [file] = Dump information about this system. --debug-trycompile = Do not delete the try_compile build tree. Only useful on one try_compile at a time. --debug-output = Put cmake in a debug mode. --trace = Put cmake in trace mode. --warn-uninitialized= Warn about uninitialized values. --warn-unused-vars = Warn about unused variables. --no-warn-unused-cli= Don't warn about command line options. --check-system-vars = Find problems with variable usage in system files. --help-command cmd [file] = Print help for a single command and exit. --help-command-list [file] = List available listfile commands and exit. --help-commands [file] = Print help for all commands and exit. --help-compatcommands [file]= Print help for compatibility commands. --help-module module [file] = Print help for a single module and exit. --help-module-list [file] = List available modules and exit. --help-modules [file] = Print help for all modules and exit. --help-custom-modules [file]= Print help for all custom modules and exit. --help-policy cmp [file]= Print help for a single policy and exit. --help-policies [file] = Print help for all policies and exit. --help-property prop [file] = Print help for a single property and exit. --help-property-list [file] = List available properties and exit. --help-properties [file]= Print help for all properties and exit. --help-variable var [file] = Print help for a single variable and exit. --help-variable-list [file] = List documented variables and exit. --help-variables [file] = Print help for all variables and exit. --copyright [file] = Print the CMake copyright and exit. --help,-help,-usage,-h,-H,/?= Print usage information and exit. --help-full [file] = Print full help and exit. --help-html [file] = Print full help in HTML format. --help-man [file] = Print full help as a UNIX man page and exit. --version,-version,/V [file]= Show program name/version banner and exit. Generators The following generators are available on this platform: Unix Makefiles = Generates standard UNIX makefiles. Ninja = Generates build.ninja files (experimental). Xcode = Generate Xcode project files. CodeBlocks - Ninja = Generates CodeBlocks project files. CodeBlocks - Unix Makefiles = Generates CodeBlocks project files. Eclipse CDT4 - Ninja= Generates Eclipse CDT 4.0 project files. Eclipse CDT4 - Unix Makefiles = Generates Eclipse CDT 4.0 project files. KDevelop3 = Generates KDevelop 3 project files. KDevelop3 - Unix Makefiles = Generates KDevelop 3 project files. Sublime Text 2 - Ninja = Generates Sublime Text 2 project files. Sublime Text 2 - Unix Makefiles = Generates Sublime Text 2 project files. Sonikas-MacBook-Pro:gromacs-4.6.2 sonikagahlawat$ ccmake ccmake version 2.8.11.1 Usage ccmake path-to-source ccmake
[gmx-users] Help with modified gmx_covar
Dear Gmx users, I need to ask you about a doubt I have regarding changing an analysis tool in Gromacs. More specifically g_covar. I found the modified source code for gmx_covar.c [ gmx_covar.c http://gromacs.5086.x6.nabble.com/file/n5008825/gmx_covar.c ] and I would like to replace the current g_covar with modified one. I copied the source code in the src/tools directory and built g_covar cp gmx_covar.c ../softwares/gromacs4.5.6/src/tools make (or make g_covar) It runs fine, but when I run g_covar again, it gives me the old options. The new one should have more flags in addition to the old ones, like: -clog -xpmc (you can find them in source code) Does anyone know if I am missing something? If someone could briefly tell me the steps, I would really appreciate it. Best Rohit -- View this message in context: http://gromacs.5086.x6.nabble.com/Help-with-modified-gmx-covar-tp5008825.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] Help with modified gmx_covar
You need to call the newly compiled code. Either install the new version and source GMXRC appropriately, or use a full path to the new version in the build tree. Mark On Wed, Jun 5, 2013 at 11:05 AM, rohitarora rohitaror...@gmail.com wrote: Dear Gmx users, I need to ask you about a doubt I have regarding changing an analysis tool in Gromacs. More specifically g_covar. I found the modified source code for gmx_covar.c [ gmx_covar.c http://gromacs.5086.x6.nabble.com/file/n5008825/gmx_covar.c ] and I would like to replace the current g_covar with modified one. I copied the source code in the src/tools directory and built g_covar cp gmx_covar.c ../softwares/gromacs4.5.6/src/tools make (or make g_covar) It runs fine, but when I run g_covar again, it gives me the old options. The new one should have more flags in addition to the old ones, like: -clog -xpmc (you can find them in source code) Does anyone know if I am missing something? If someone could briefly tell me the steps, I would really appreciate it. Best Rohit -- View this message in context: http://gromacs.5086.x6.nabble.com/Help-with-modified-gmx-covar-tp5008825.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 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] help with g_hydorder and g_polystat
That's ok. Thank you for your help. In the meantime, I might see if g_h2order is a good substitute for g_hydorder. Kind Regards, Alaina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 01 May 2013 22:58 To: Discussion list for GROMACS users Subject: Re: [gmx-users] help with g_hydorder and g_polystat On 5/1/13 8:44 AM, Emmanuel, Alaina wrote: No, using a trajectory file with g_hydorder hasn't made any difference. The error is still the same. When I use g_polystat, I use the following command: g_polystat_d -f file.xtc -s file.tpr -n polymer_backbone.ndx -p persist.xvg -o polystat.xvg Note: Using polymer_backbone.ndx yields fewer polymers with nan issues, than using the whole polymer structure in an index file. The g_hydorder problem is a bug in the code and I have filed a bug report on Redmine. I have no insight into what's going on with g_polystat, sorry. -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 -- 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] help with g_hydorder and g_polystat
On 4/30/13 9:00 PM, Emmanuel, Alaina wrote: Hello Justin, My mdp file shows that the pbc was set to xyz. Instead of analyzing a coordinate file, does it work with a trajectory? Regarding g_polystat and the nan's, what command are you issuing? -Justin Kind Regards, Alaina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 30 April 2013 16:10 To: Discussion list for GROMACS users Subject: Re: [gmx-users] help with g_hydorder and g_polystat On 4/30/13 6:24 AM, Emmanuel, Alaina wrote: Dear All, I'm fairly new to gromacs and having a bit of problem with the g_hydorder and g_polystat. Thanks in advanced for your time. For g_hydorder, I get a fatal error when I type the following command: g_hydorder_d -f file.gro -s file.tpr -n waters.ndx -o file1.xpm file2.xpm Error: Internal error in pbc_dx, set pbc has nor been called For more information.. I'm not sure what this means. It seems to be implying that I don't have a box around my polymer, but the gro file clearly shows that my box is 4.94 x 4.94 x 4.94. Any ideas? What is your setting for the pbc keyword in the .mdp file? For g_polystat, I'm a bit worried about the persistence lengths that I get for short polymers. With repeat units smaller than 50 these usually show nan values, that cannot be plotted. From reading the gmx threads I've found that Nan stands for Not a Number, but why do these nan values appear and how can I prevent it so that I can read in my results? This could be an underlying problem related to the above interpretation of periodicity. We don't have enough information to say for sure yet. -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 -- 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] help with g_hydorder and g_polystat
No, using a trajectory file with g_hydorder hasn't made any difference. The error is still the same. When I use g_polystat, I use the following command: g_polystat_d -f file.xtc -s file.tpr -n polymer_backbone.ndx -p persist.xvg -o polystat.xvg Note: Using polymer_backbone.ndx yields fewer polymers with nan issues, than using the whole polymer structure in an index file. Kind Regards, Alaina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 01 May 2013 10:58 To: Discussion list for GROMACS users Subject: Re: [gmx-users] help with g_hydorder and g_polystat On 4/30/13 9:00 PM, Emmanuel, Alaina wrote: Hello Justin, My mdp file shows that the pbc was set to xyz. Instead of analyzing a coordinate file, does it work with a trajectory? Regarding g_polystat and the nan's, what command are you issuing? -Justin Kind Regards, Alaina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 30 April 2013 16:10 To: Discussion list for GROMACS users Subject: Re: [gmx-users] help with g_hydorder and g_polystat On 4/30/13 6:24 AM, Emmanuel, Alaina wrote: Dear All, I'm fairly new to gromacs and having a bit of problem with the g_hydorder and g_polystat. Thanks in advanced for your time. For g_hydorder, I get a fatal error when I type the following command: g_hydorder_d -f file.gro -s file.tpr -n waters.ndx -o file1.xpm file2.xpm Error: Internal error in pbc_dx, set pbc has nor been called For more information.. I'm not sure what this means. It seems to be implying that I don't have a box around my polymer, but the gro file clearly shows that my box is 4.94 x 4.94 x 4.94. Any ideas? What is your setting for the pbc keyword in the .mdp file? For g_polystat, I'm a bit worried about the persistence lengths that I get for short polymers. With repeat units smaller than 50 these usually show nan values, that cannot be plotted. From reading the gmx threads I've found that Nan stands for Not a Number, but why do these nan values appear and how can I prevent it so that I can read in my results? This could be an underlying problem related to the above interpretation of periodicity. We don't have enough information to say for sure yet. -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 -- 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 -- 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] help with g_hydorder and g_polystat
On 5/1/13 8:44 AM, Emmanuel, Alaina wrote: No, using a trajectory file with g_hydorder hasn't made any difference. The error is still the same. When I use g_polystat, I use the following command: g_polystat_d -f file.xtc -s file.tpr -n polymer_backbone.ndx -p persist.xvg -o polystat.xvg Note: Using polymer_backbone.ndx yields fewer polymers with nan issues, than using the whole polymer structure in an index file. The g_hydorder problem is a bug in the code and I have filed a bug report on Redmine. I have no insight into what's going on with g_polystat, sorry. -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
[gmx-users] help with g_hydorder and g_polystat
Dear All, I'm fairly new to gromacs and having a bit of problem with the g_hydorder and g_polystat. Thanks in advanced for your time. For g_hydorder, I get a fatal error when I type the following command: g_hydorder_d -f file.gro -s file.tpr -n waters.ndx -o file1.xpm file2.xpm Error: Internal error in pbc_dx, set pbc has nor been called For more information.. I'm not sure what this means. It seems to be implying that I don't have a box around my polymer, but the gro file clearly shows that my box is 4.94 x 4.94 x 4.94. Any ideas? For g_polystat, I'm a bit worried about the persistence lengths that I get for short polymers. With repeat units smaller than 50 these usually show nan values, that cannot be plotted. From reading the gmx threads I've found that Nan stands for Not a Number, but why do these nan values appear and how can I prevent it so that I can read in my results? Again, thank you for your help. Kind Regards, Alaina -- 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] help with g_hydorder and g_polystat
On 4/30/13 6:24 AM, Emmanuel, Alaina wrote: Dear All, I'm fairly new to gromacs and having a bit of problem with the g_hydorder and g_polystat. Thanks in advanced for your time. For g_hydorder, I get a fatal error when I type the following command: g_hydorder_d -f file.gro -s file.tpr -n waters.ndx -o file1.xpm file2.xpm Error: Internal error in pbc_dx, set pbc has nor been called For more information.. I'm not sure what this means. It seems to be implying that I don't have a box around my polymer, but the gro file clearly shows that my box is 4.94 x 4.94 x 4.94. Any ideas? What is your setting for the pbc keyword in the .mdp file? For g_polystat, I'm a bit worried about the persistence lengths that I get for short polymers. With repeat units smaller than 50 these usually show nan values, that cannot be plotted. From reading the gmx threads I've found that Nan stands for Not a Number, but why do these nan values appear and how can I prevent it so that I can read in my results? This could be an underlying problem related to the above interpretation of periodicity. We don't have enough information to say for sure yet. -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] help with g_hydorder and g_polystat
Hello Justin, My mdp file shows that the pbc was set to xyz. Kind Regards, Alaina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 30 April 2013 16:10 To: Discussion list for GROMACS users Subject: Re: [gmx-users] help with g_hydorder and g_polystat On 4/30/13 6:24 AM, Emmanuel, Alaina wrote: Dear All, I'm fairly new to gromacs and having a bit of problem with the g_hydorder and g_polystat. Thanks in advanced for your time. For g_hydorder, I get a fatal error when I type the following command: g_hydorder_d -f file.gro -s file.tpr -n waters.ndx -o file1.xpm file2.xpm Error: Internal error in pbc_dx, set pbc has nor been called For more information.. I'm not sure what this means. It seems to be implying that I don't have a box around my polymer, but the gro file clearly shows that my box is 4.94 x 4.94 x 4.94. Any ideas? What is your setting for the pbc keyword in the .mdp file? For g_polystat, I'm a bit worried about the persistence lengths that I get for short polymers. With repeat units smaller than 50 these usually show nan values, that cannot be plotted. From reading the gmx threads I've found that Nan stands for Not a Number, but why do these nan values appear and how can I prevent it so that I can read in my results? This could be an underlying problem related to the above interpretation of periodicity. We don't have enough information to say for sure yet. -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 -- 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] help with g_hydorder and g_polystat
Hello Justin, My mdp file shows that the pbc was set to xyz. Kind Regards, Alaina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 30 April 2013 16:10 To: Discussion list for GROMACS users Subject: Re: [gmx-users] help with g_hydorder and g_polystat On 4/30/13 6:24 AM, Emmanuel, Alaina wrote: Dear All, I'm fairly new to gromacs and having a bit of problem with the g_hydorder and g_polystat. Thanks in advanced for your time. For g_hydorder, I get a fatal error when I type the following command: g_hydorder_d -f file.gro -s file.tpr -n waters.ndx -o file1.xpm file2.xpm Error: Internal error in pbc_dx, set pbc has nor been called For more information.. I'm not sure what this means. It seems to be implying that I don't have a box around my polymer, but the gro file clearly shows that my box is 4.94 x 4.94 x 4.94. Any ideas? What is your setting for the pbc keyword in the .mdp file? For g_polystat, I'm a bit worried about the persistence lengths that I get for short polymers. With repeat units smaller than 50 these usually show nan values, that cannot be plotted. From reading the gmx threads I've found that Nan stands for Not a Number, but why do these nan values appear and how can I prevent it so that I can read in my results? This could be an underlying problem related to the above interpretation of periodicity. We don't have enough information to say for sure yet. -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 -- 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] help: load imbalance
Hello, I wanna ask some questions about load imbalance. 1 Here are the messages resulted from grompp -f md.mdp -p topol.top -c npt.gro -o md.tpr NOTE 1 [file md.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing therefore, i changed the md.mdp as whrited below, then used the command grompp -f md.mdp -p topol.top -c npt.gro -o md.tpr , then there is no NOTE printed. So if i change the cut-offs to 2.0 nm and increase the grid spacing to 0.30, does the calculated results reasonable? ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 2 ; short-range neighborlist cutoff (in nm) rcoulomb= 2 ; short-range electrostatic cutoff (in nm) rvdw= 2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.3 ; grid spacing for FFT 2 and how about no changes, just simulate it with the original mdp. Is the results still reasonable? Here are the messages without any changes: DD load balancing is limited by minimum cell size in dimension X DD step 2933999 vol min/aver 0.189! load imb.: force 124.7% Step Time Lambda 2934000 5868.00.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. LJ-14 Coulomb-14 2.99315e+022.13778e+011.74659e+022.22024e+022.02466e+03 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential -1.68074e+02 -2.09809e-01 -1.80294e+03 -3.28155e+03 -2.51074e+03 Kinetic En. Total EnergyTemperature Pres. DC (bar) Pressure (bar) 1.69264e+041.44156e+042.95552e+02 -1.33866e-041.51489e+00 Constr. rmsd 2.60082e-05 -- 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] help: load imbalance
On Wed, Apr 10, 2013 at 10:50 AM, 申昊 shen...@mail.bnu.edu.cn wrote: Hello, I wanna ask some questions about load imbalance. 1 Here are the messages resulted from grompp -f md.mdp -p topol.top -c npt.gro -o md.tpr NOTE 1 [file md.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing therefore, i changed the md.mdp as whrited below, then used the command grompp -f md.mdp -p topol.top -c npt.gro -o md.tpr , then there is no NOTE printed. So if i change the cut-offs to 2.0 nm and increase the grid spacing to 0.30, does the calculated results reasonable? No. You're making ad hoc changes to nonbonded cutoffs (which can completely invalidate the force field model) and you're making the PME grid less accurate. -Justin ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 2 ; short-range neighborlist cutoff (in nm) rcoulomb= 2 ; short-range electrostatic cutoff (in nm) rvdw= 2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.3 ; grid spacing for FFT 2 and how about no changes, just simulate it with the original mdp. Is the results still reasonable? Here are the messages without any changes: DD load balancing is limited by minimum cell size in dimension X DD step 2933999 vol min/aver 0.189! load imb.: force 124.7% Step Time Lambda 2934000 5868.00.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. LJ-14 Coulomb-14 2.99315e+022.13778e+011.74659e+022.22024e+022.02466e+03 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential -1.68074e+02 -2.09809e-01 -1.80294e+03 -3.28155e+03 -2.51074e+03 Kinetic En. Total EnergyTemperature Pres. DC (bar) Pressure (bar) 1.69264e+041.44156e+042.95552e+02 -1.33866e-041.51489e+00 Constr. rmsd 2.60082e-05 -- 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 -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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] help: load imbalance
On Wed, Apr 10, 2013 at 4:50 PM, 申昊 shen...@mail.bnu.edu.cn wrote: Hello, I wanna ask some questions about load imbalance. 1 Here are the messages resulted from grompp -f md.mdp -p topol.top -c npt.gro -o md.tpr NOTE 1 [file md.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing therefore, i changed the md.mdp as whrited below, then used the command grompp -f md.mdp -p topol.top -c npt.gro -o md.tpr , then there is no NOTE printed. So if i change the cut-offs to 2.0 nm and increase the grid spacing to 0.30, does the calculated results reasonable? You can shift work between short- and long-range electrostatics by adjusting the *coulomb* cut-off freely, but *not* the VdW cut-off. However, 2.0 nm sounds like a *very* long cut-off. ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 2 ; short-range neighborlist cutoff (in nm) rcoulomb= 2 ; short-range electrostatic cutoff (in nm) rvdw= 2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.3 ; grid spacing for FFT 2 and how about no changes, just simulate it with the original mdp. Is the results still reasonable? Here are the messages without any changes: DD load balancing is limited by minimum cell size in dimension X DD step 2933999 vol min/aver 0.189! load imb.: force 124.7% You are simply pushing your simulation to the limit of how far it can be parallelized. As you can see from the above output, to compensate for the imbalance, the load balancing shrunk DD cells to the extent that the volume ratio of the smallest and average DD cell size is 0.189, meaning that the smallest DD cells are ~5.3x smaller than the average cell size - and the run is still *hugely* imbalanced. The ! indicates what the line before says, that the DD load-balancing is limited and can't shrink cells further. Some aspects that might be limiting your simulation are: i) running with just a few hundred atoms/core; ii) running on multiple very different cluster nodes; iii) using a very inhomogeneous system. If you're using the group scheme (which i assume you are, otherwise the automated PP-PME balancing would have kicked in), you should be able to get better performance at high parallelization with the verlet scheme. Cheers, -- Szilard Step Time Lambda 2934000 5868.00.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. LJ-14 Coulomb-14 2.99315e+022.13778e+011.74659e+022.22024e+022.02466e+03 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential -1.68074e+02 -2.09809e-01 -1.80294e+03 -3.28155e+03 -2.51074e+03 Kinetic En. Total EnergyTemperature Pres. DC (bar) Pressure (bar) 1.69264e+041.44156e+042.95552e+02 -1.33866e-041.51489e+00 Constr. rmsd 2.60082e-05 -- 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] help with chromophore of a GFP
Dear Justin, there is not a unique GFP chromophore, the chromophore I am dealing with is not the same for which CHARMM parameters have been published (I am aware of CHARMM parameters for p-hydroxybenzylideneimidazolinone chromophore of green fluorescent protein published by Reuter et al 2002, of OPLS-AA parameters for DsRed fluorescent protein chromophore as a residue of [(4cis)2[(1cis)4 amino4oxobutanimidoyl]4(4hydroxybenzylidene)5oxo4,5dihydro1Himidazol1yl]acetic acid, of other parameters of other GFP chromophores), but mine is different: is of the same family of proteins, but different residues are involved and different heterocycles are generated. Since I have to recalculate parameters, I chose Amber ff because I already used it and I have tools to calculate Amber parameters, whereas I have no tools to calculate CHARMM parameters. In a preliminary assay, I tried to do the same parameterization using Gromos ff and PRODRG to obtain parameters and topology (apart from the fact that charges are probably wrong), but I experimented the same problem. I am talking not only about the problem of obtaining parameters for this particular chromophore, mine is a more general question: how to deal with a HETATM entry which is not a ligand, but it's a part of the protein chain? I tried to follow indications to make a new .rtp entry in the GROMACS HowTo's, probably my problem would be solved if I would be able to modify the aminoacids.hdb file, but this is not a simple modification of a residue (eg. an oxidised Met or a methylation of a Lys), this is a profound modification of four residues, so how can I deal with this? I had a look at the .hdb file, but hydrogens I can see are typical for amino acids residues and I cannot find any suggestions on how to treat hydrogens that are bound to a residue which is so different from classic standard residues. Has anyone made this before (I am sure yes)? Could you please give some suggestions? Thank you very much Anna __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Ponte don Melillo 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089 969603 E-mail: amarabo...@unisa.it Skype: annam1972 When a man with a gun meets a man with a pen, the man with the gun is a dead man (Roberto Benigni, about Roberto Saviano) Il 21/03/2013 06:37, gmx-users-requ...@gromacs.org ha scritto: Message: 3 Date: Wed, 20 Mar 2013 13:05:08 -0400 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] help with chromophore of a GFP To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: CADUqwc5C+2NZWrwvzHh11Wnd=shwnhyqttvophzkwweoeg9...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 On Wed, Mar 20, 2013 at 1:01 PM, Anna MARABOTTI amarabo...@unisa.it wrote: Dear gmx-users, it's about two weeks that I'm trying to solve this problem, and I can't, so I'm asking your help. I want to do some MD simulations on a protein of the family of green fluorescent protein. This protein, as you know, has a chromophore (CFY) derived from four residues of the protein (F64-C65-Y66-G67) and covalently bound to the rest of the protein chain. How to parametrize this object, since it is not recognized by pdb2gmx? I looked at the gmx-users list and the suggestion was to create a new entry in the .rtp file of the selected forcefield. I decided to use Amber99SB since it seemed the better for my scope, then I start trying to parameterize it. This is what I did: * I used Pymol to add H to my pdb file, since I want to use an all H forcefield and since Antechamber (see below) does not work without H * I extracted the segment V63-CFY-H68 from my .pdb file. I did this since, when I extracted CFY only, I had problems with the terminals * Following the Antechamber tutorial, I used Antechamber (using the traditional Amber force field, not GAFF) to calculate charges and to assign atom types to this segment. * I used these calculated parameters in order to add the CFY residue to aminoacids.rtp in amber99sb.ff directory. * I tried to modify also aminoacids.hdb, but since it seemed too complicated to me, I decided to keep it unchanged, and to give pdb2gmx the protein with H already present * No need to add new atom/bond types to ffbonded.itp and ffnonbonded.itp: they seem all present. Since CFY is bound to the rest of protein with common peptide bonds, I did not change specbond.dat either. * I added CFY in residuetypes.dat with the specification Protein In my opinion, all was ready to go, instead... When I launched pdb2gmx to my protein with H added by PyMol, I got immediately an error: Fatal error: Atom H01 in residue SER 3 was not found in rtp entry NSER with 13 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might
Re: [gmx-users] help with chromophore of a GFP
On Wed, Mar 20, 2013 at 6:01 PM, Anna MARABOTTI amarabo...@unisa.it wrote: Dear gmx-users, it's about two weeks that I'm trying to solve this problem, and I can't, so I'm asking your help. I want to do some MD simulations on a protein of the family of green fluorescent protein. This protein, as you know, has a chromophore (CFY) derived from four residues of the protein (F64-C65-Y66-G67) and covalently bound to the rest of the protein chain. How to parametrize this object, since it is not recognized by pdb2gmx? I looked at the gmx-users list and the suggestion was to create a new entry in the .rtp file of the selected forcefield. Indeed, this kind of problem is most easily solved by making a new residue that contains the whole chromophore, such that it links to its neighbours with normal peptide links. I decided to use Amber99SB since it seemed the better for my scope, then I start trying to parameterize it. This is what I did: * I used Pymol to add H to my pdb file, since I want to use an all H forcefield and since Antechamber (see below) does not work without H * I extracted the segment V63-CFY-H68 from my .pdb file. I did this since, when I extracted CFY only, I had problems with the terminals * Following the Antechamber tutorial, I used Antechamber (using the traditional Amber force field, not GAFF) to calculate charges and to assign atom types to this segment. * I used these calculated parameters in order to add the CFY residue to aminoacids.rtp in amber99sb.ff directory. * I tried to modify also aminoacids.hdb, but since it seemed too complicated to me, I decided to keep it unchanged, and to give pdb2gmx the protein with H already present * No need to add new atom/bond types to ffbonded.itp and ffnonbonded.itp: they seem all present. Since CFY is bound to the rest of protein with common peptide bonds, I did not change specbond.dat either. * I added CFY in residuetypes.dat with the specification Protein In my opinion, all was ready to go, instead... When I launched pdb2gmx to my protein with H added by PyMol, I got immediately an error: Fatal error: Atom H01 in residue SER 3 was not found in rtp entry NSER with 13 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors [1] From this error I understand that: * the code for H in PyMol is different from the code for H in Amber (read from aminoacids.rtp); in order to correct this error, I should add -ignh in order to ignore H in input. pdb2gmx has to be able to make sense of the atom naming. There are lots of different conventions for how to name atoms, particularly hydrogen atoms. pdb2gmx can't possibly encode the logic to convert all of those conventions. So the path of least resistance can be to ignore hydrogens and regenerate them according to the generation rules. However, you can just rename them in the input file so that pdb2gmx understands your meaning. The NSER entry in the .rtp file shows you the names pdb2gmx expects. If you edit the names of those hydrogen atoms (probably H01, H02, H03) in your input coordinate file accordingly (to H1, H2, H3), things will be fine. Be sure you don't break the required column formatting of the coordinate file! * If I add -ignh, all the H of CFY will be ignored too, and I will not be able to add them since I did not modify aminoacids.hdb * since I made calculations on CFY with H added by PyMol, probably also my codes for H will be wrong. Your atom names for CFY in the .rtp and the input coordinate file will have to match. How you want to achieve that is up to you. * If I use reduce (the Amber tool to add H, as suggested by the tutorial) to add H to my protein, it does not add H to CFY because it complaints that the residue is not in HETATM connection database (but the record CONECT is present in .pdb file). If I add H to CFY alone, I have problems with the terminals. My question is, obviously: how can I parameterize this chromophore correctly? Please give me, if possible, some step-by-step indications on what to do. I made dozens of trials, ALL with errors, and I really do not know how to do. You're very much on the right track. Your decision to use Pymol to generate main chain hydrogens rather than teach pdb2gmx how to generate CFY hydrogens had consequences that you are now dealing with. In a
Re: [gmx-users] help with chromophore of a GFP
3.146 2.112 2.205 2.935 2.272 3.263 1.402 HIS172 CYS174 MET189 HIS193 HIS197 NE22588 SG2623 SD2891 NE22942 NE23011 CYS174 SG2623 0.826 MET189 SD2891 3.417 2.599 HIS193 NE22942 2.831 2.079 1.020 HIS197 NE23011 2.011 1.324 1.766 0.939 HIS217 NE23329 2.629 2.068 1.936 0.946 1.003 Opening force field file ./amber99sb.ff/aminoacids.arn Opening force field file ./amber99sb.ff/dna.arn Opening force field file ./amber99sb.ff/rna.arn Checking for duplicate atoms Now there are 3345 atoms. Deleted 1 duplicates. Now there are 213 residues with 3345 atoms Making bonds... Warning: Long Bond (988-989 = 0.453624 nm) WARNING: atom O1 is missing in residue CFY 66 in the pdb file --- Program pdb2gmx_d, VERSION 4.5.4 Source code file: pdb2top.c, line: 1463 Fatal error: There were 1 missing atoms in molecule Protein_chain_A, if you want to use this incomplete topology anyhow, use the option -missing For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors The strange thing is that I checked for this error, but atom O1 in residue CFY66 is present BOTH in the starting .pdb file (the one I used for pdb2gmx) AND in the aminoacids.rtp file I checked 4 or 5 times, every time erasing the old file, checking the file IMMEDIATELY BEFORE submitting it to pdb2gmx. All atoms present in aminoacids.rtp for CFY residue are also present in the .pdb file and vice versa, and I am sure I did not make the stupid error of naming the atom 01 (zero-one) instead of O1 (o-one). I suspect that this atom is the one which is deleted because recognized as duplicated, but I'm not sure about it and I don't know how to check it. I am sure there are no duplicated atoms in CFY. I feel like this is a fake error message (i.e.: there is an error in my files, but it is not the one that is reported in the message: probably a problem occur around this atom, but it is not exactly ON this atom). However, I am not able to find errors. BTW the long bond of the other warning message is not involving residue CFY. Any help is welcome Thank you so much. Anna Il 21.03.2013 12:00 gmx-users-requ...@gromacs.org ha scritto: Dear gmx-users, it's about two weeks that I'm trying to solve this problem, and I can't, so I'm asking your help. I want to do some MD simulations on a protein of the family of green fluorescent protein. This protein, as you know, has a chromophore (CFY) derived from four residues of the protein (F64-C65-Y66-G67) and covalently bound to the rest of the protein chain. How to parametrize this object, since it is not recognized by pdb2gmx? I looked at the gmx-users list and the suggestion was to create a new entry in the .rtp file of the selected forcefield. Indeed, this kind of problem is most easily solved by making a new residue that contains the whole chromophore, such that it links to its neighbours with normal peptide links. -- Message: 5 Date: Thu, 21 Mar 2013 11:46:12 +0100 From: Mark Abraham mark.j.abra...@gmail.com [2] Subject: Re: [gmx-users] help with chromophore of a GFP To: Discussion list for GROMACS users gmx-users@gromacs.org [3] Message-ID: camnumasicymgivb_x5sy1yb44th8vknioqvhzdqq-tam9tn...@mail.gmail.com [4] Content-Type: text/plain; charset=ISO-8859-1 On Wed, Mar 20, 2013 at 6:01 PM, Anna MARABOTTI amarabo...@unisa.it [5] wrote: I decided to use Amber99SB since it seemed the better for my scope, then I start trying to parameterize it. This is what I did: * I used Pymol to add H to my pdb file, since I want to use an all H forcefield and since Antechamber (see below) does not work without H * I extracted the segment V63-CFY-H68 from my .pdb file. I did this since, when I extracted CFY only, I had problems with the terminals * Following the Antechamber tutorial, I used Antechamber (using the traditional Amber force field, not GAFF) to calculate charges and to assign atom types to this segment. * I used these calculated parameters in order to add the CFY residue to aminoacids.rtp in amber99sb.ff directory. * I tried to modify also aminoacids.hdb, but since it seemed too complicated to me, I decided to keep it unchanged, and to give pdb2gmx the protein with H already present * No need to add new atom/bond types to ffbonded.itp and ffnonbonded.itp: they seem all present. Since CFY is bound to the rest of protein with common peptide bonds, I did not change specbond.dat either. * I added CFY in residuetypes.dat with the specification Protein In my opinion, all was ready to go, instead... When I launched pdb2gmx to my protein with H added by PyMol, I got immediately an error: Fatal error: Atom H01 in residue SER 3 was not found in rtp entry NSER with 13 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only
Re: [gmx-users] help with chromophore of a GFP
2.152 1.681 1.297 0.745 MET189 SD2891 3.547 2.310 1.858 1.893 1.980 3.627 2.290 HIS193 NE22942 3.076 1.890 1.639 2.197 1.760 3.221 1.547 HIS197 NE23011 2.229 1.149 1.407 2.078 1.323 2.401 0.676 HIS217 NE23329 3.146 2.112 2.205 2.935 2.272 3.263 1.402 HIS172 CYS174 MET189 HIS193 HIS197 NE22588 SG2623 SD2891 NE22942 NE23011 CYS174 SG2623 0.826 MET189 SD2891 3.417 2.599 HIS193 NE22942 2.831 2.079 1.020 HIS197 NE23011 2.011 1.324 1.766 0.939 HIS217 NE23329 2.629 2.068 1.936 0.946 1.003 Opening force field file ./amber99sb.ff/aminoacids.arn Opening force field file ./amber99sb.ff/dna.arn Opening force field file ./amber99sb.ff/rna.arn Checking for duplicate atoms Now there are 3345 atoms. Deleted 1 duplicates. Now there are 213 residues with 3345 atoms Making bonds... Warning: Long Bond (988-989 = 0.453624 nm) WARNING: atom O1 is missing in residue CFY 66 in the pdb file --- Program pdb2gmx_d, VERSION 4.5.4 Source code file: pdb2top.c, line: 1463 Fatal error: There were 1 missing atoms in molecule Protein_chain_A, if you want to use this incomplete topology anyhow, use the option -missing For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors The strange thing is that I checked for this error, but atom O1 in residue CFY66 is present BOTH in the starting .pdb file (the one I used for pdb2gmx) AND in the aminoacids.rtp file I checked 4 or 5 times, every time erasing the old file, checking the file IMMEDIATELY BEFORE submitting it to pdb2gmx. All atoms present in aminoacids.rtp for CFY residue are also present in the .pdb file and vice versa, and I am sure I did not make the stupid error of naming the atom 01 (zero-one) instead of O1 (o-one). I suspect that this atom is the one which is deleted because recognized as duplicated, but I'm not sure about it and I don't know how to check it. I am sure there are no duplicated atoms in CFY. I feel like this is a fake error message (i.e.: there is an error in my files, but it is not the one that is reported in the message: probably a problem occur around this atom, but it is not exactly ON this atom). However, I am not able to find errors. This is indeed a false error. It comes from the fact that pdb2gmx interprets anything named O1 or O2 as C-terminal atoms. Use any other name you like aside from O1 or O2. -Justin BTW the long bond of the other warning message is not involving residue CFY. Any help is welcome Thank you so much. Anna Il 21.03.2013 12:00 gmx-users-requ...@gromacs.org ha scritto: Dear gmx-users, it's about two weeks that I'm trying to solve this problem, and I can't, so I'm asking your help. I want to do some MD simulations on a protein of the family of green fluorescent protein. This protein, as you know, has a chromophore (CFY) derived from four residues of the protein (F64-C65-Y66-G67) and covalently bound to the rest of the protein chain. How to parametrize this object, since it is not recognized by pdb2gmx? I looked at the gmx-users list and the suggestion was to create a new entry in the .rtp file of the selected forcefield. Indeed, this kind of problem is most easily solved by making a new residue that contains the whole chromophore, such that it links to its neighbours with normal peptide links. -- Message: 5 Date: Thu, 21 Mar 2013 11:46:12 +0100 From: Mark Abraham mark.j.abra...@gmail.com [2] Subject: Re: [gmx-users] help with chromophore of a GFP To: Discussion list for GROMACS users gmx-users@gromacs.org [3] Message-ID: camnumasicymgivb_x5sy1yb44th8vknioqvhzdqq-tam9tn...@mail.gmail.com [4] Content-Type: text/plain; charset=ISO-8859-1 On Wed, Mar 20, 2013 at 6:01 PM, Anna MARABOTTI amarabo...@unisa.it [5] wrote: I decided to use Amber99SB since it seemed the better for my scope, then I start trying to parameterize it. This is what I did: * I used Pymol to add H to my pdb file, since I want to use an all H forcefield and since Antechamber (see below) does not work without H * I extracted the segment V63-CFY-H68 from my .pdb file. I did this since, when I extracted CFY only, I had problems with the terminals * Following the Antechamber tutorial, I used Antechamber (using the traditional Amber force field, not GAFF) to calculate charges and to assign atom types to this segment. * I used these calculated parameters in order to add the CFY residue to aminoacids.rtp in amber99sb.ff directory. * I tried to modify also aminoacids.hdb, but since it seemed too complicated to me, I decided to keep it unchanged, and to give pdb2gmx the protein with H already present * No need to add new atom/bond types to ffbonded.itp and ffnonbonded.itp: they seem all present. Since CFY is bound to the rest of protein with common peptide bonds, I did not change specbond.dat
Re: [gmx-users] help with chromophore of a GFP
HIS119 NE21803 1.688 0.976 0.584 1.078 MET135 SD2041 1.057 1.365 2.661 2.490 2.119 MET162 SD2439 1.878 0.871 1.805 2.246 1.520 1.861 HIS172 NE22588 1.721 1.401 2.829 2.860 2.359 1.067 1.342 CYS174 SG2623 1.694 0.725 2.140 2.152 1.681 1.297 0.745 MET189 SD2891 3.547 2.310 1.858 1.893 1.980 3.627 2.290 HIS193 NE22942 3.076 1.890 1.639 2.197 1.760 3.221 1.547 HIS197 NE23011 2.229 1.149 1.407 2.078 1.323 2.401 0.676 HIS217 NE23329 3.146 2.112 2.205 2.935 2.272 3.263 1.402 HIS172 CYS174 MET189 HIS193 HIS197 NE22588 SG2623 SD2891 NE22942 NE23011 CYS174 SG2623 0.826 MET189 SD2891 3.417 2.599 HIS193 NE22942 2.831 2.079 1.020 HIS197 NE23011 2.011 1.324 1.766 0.939 HIS217 NE23329 2.629 2.068 1.936 0.946 1.003 Opening force field file ./amber99sb.ff/aminoacids.arn Opening force field file ./amber99sb.ff/dna.arn Opening force field file ./amber99sb.ff/rna.arn Checking for duplicate atoms Now there are 3345 atoms. Deleted 1 duplicates. That also looks suspicious. Now there are 213 residues with 3345 atoms Making bonds... Warning: Long Bond (988-989 = 0.453624 nm) That seems like it might be a peptide bond bridging a gap where pdb2gmx was unable to recognize the intervening content as a peptide residue. WARNING: atom O1 is missing in residue CFY 66 in the pdb file --- Program pdb2gmx_d, VERSION 4.5.4 Source code file: pdb2top.c, line: 1463 Fatal error: There were 1 missing atoms in molecule Protein_chain_A, if you want to use this incomplete topology anyhow, use the option -missing For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors The strange thing is that I checked for this error, but atom O1 in residue CFY66 is present BOTH in the starting .pdb file (the one I used for pdb2gmx) AND in the aminoacids.rtp file I checked 4 or 5 times, every time erasing the old file, checking the file IMMEDIATELY BEFORE submitting it to pdb2gmx. All atoms present in aminoacids.rtp for CFY residue are also present in the .pdb file and vice versa, and I am sure I did not make the stupid error of naming the atom 01 (zero-one) instead of O1 (o-one). I suspect that this atom is the one which is deleted because recognized as duplicated, but I'm not sure about it and I don't know how to check it. I am sure there are no duplicated atoms in CFY. I feel like this is a fake error message (i.e.: there is an error in my files, but it is not the one that is reported in the message: probably a problem occur around this atom, but it is not exactly ON this atom). However, I am not able to find errors. Hmm that seems weird. Justin's theory sounds plausible, but I haven't seen someone stumble on that before. Also plausible is that pdb2gmx thinks your CFY is a disconnected part of the chain and needs terminating (which might happen with an oxygen named O1?). It's possible there's buggy behaviour here that has been fixed in the two years since that code was released. There certainly has been an upgrade of the is this really a new chain machinery. Unless you have a strong scientific reason to keep 4.5.4, I'd switch to 4.6.1 (or 4.5.6 if you really have to keep 4.5). If Justin's fix doesn't work, and you have problems with a more recent version, then we can look closer. BTW the long bond of the other warning message is not involving residue CFY. Yeah, but my bet is those atoms are the C-terminus and N-terminus of the fragments that should form peptide bonds to CFY. Mark Any help is welcome Thank you so much. Anna Il 21.03.2013 12:00 gmx-users-requ...@gromacs.org ha scritto: Dear gmx-users, it's about two weeks that I'm trying to solve this problem, and I can't, so I'm asking your help. I want to do some MD simulations on a protein of the family of green fluorescent protein. This protein, as you know, has a chromophore (CFY) derived from four residues of the protein (F64-C65-Y66-G67) and covalently bound to the rest of the protein chain. How to parametrize this object, since it is not recognized by pdb2gmx? I looked at the gmx-users list and the suggestion was to create a new entry in the .rtp file of the selected forcefield. Indeed, this kind of problem is most easily solved by making a new residue that contains the whole chromophore, such that it links to its neighbours with normal peptide links. -- Message: 5 Date: Thu, 21 Mar 2013 11:46:12 +0100 From: Mark Abraham mark.j.abra...@gmail.com [2] Subject: Re: [gmx-users] help with chromophore of a GFP To: Discussion list for GROMACS users gmx-users@gromacs.org [3] Message-ID: camnumasicymgivb_x5sy1yb44th8vknioqvhzdqq-tam9tn...@mail.gmail.com [4] Content-Type: text/plain; charset=ISO-8859-1 On Wed, Mar 20, 2013 at 6:01 PM, Anna MARABOTTI amarabo...@unisa.it [5] wrote: I decided to use Amber99SB
Re: [gmx-users] help with chromophore of a GFP
2.661 2.490 2.119 MET162 SD2439 1.878 0.871 1.805 2.246 1.520 1.861 HIS172 NE22588 1.721 1.401 2.829 2.860 2.359 1.067 1.342 CYS174 SG2623 1.694 0.725 2.140 2.152 1.681 1.297 0.745 MET189 SD2891 3.547 2.310 1.858 1.893 1.980 3.627 2.290 HIS193 NE22942 3.076 1.890 1.639 2.197 1.760 3.221 1.547 HIS197 NE23011 2.229 1.149 1.407 2.078 1.323 2.401 0.676 HIS217 NE23329 3.146 2.112 2.205 2.935 2.272 3.263 1.402 HIS172 CYS174 MET189 HIS193 HIS197 NE22588 SG2623 SD2891 NE22942 NE23011 CYS174 SG2623 0.826 MET189 SD2891 3.417 2.599 HIS193 NE22942 2.831 2.079 1.020 HIS197 NE23011 2.011 1.324 1.766 0.939 HIS217 NE23329 2.629 2.068 1.936 0.946 1.003 Opening force field file ./amber99sb.ff/aminoacids.arn Opening force field file ./amber99sb.ff/dna.arn Opening force field file ./amber99sb.ff/rna.arn Checking for duplicate atoms Now there are 3345 atoms. Deleted 1 duplicates. That also looks suspicious. Now there are 213 residues with 3345 atoms Making bonds... Warning: Long Bond (988-989 = 0.453624 nm) That seems like it might be a peptide bond bridging a gap where pdb2gmx was unable to recognize the intervening content as a peptide residue. WARNING: atom O1 is missing in residue CFY 66 in the pdb file --- Program pdb2gmx_d, VERSION 4.5.4 Source code file: pdb2top.c, line: 1463 Fatal error: There were 1 missing atoms in molecule Protein_chain_A, if you want to use this incomplete topology anyhow, use the option -missing For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors The strange thing is that I checked for this error, but atom O1 in residue CFY66 is present BOTH in the starting .pdb file (the one I used for pdb2gmx) AND in the aminoacids.rtp file I checked 4 or 5 times, every time erasing the old file, checking the file IMMEDIATELY BEFORE submitting it to pdb2gmx. All atoms present in aminoacids.rtp for CFY residue are also present in the .pdb file and vice versa, and I am sure I did not make the stupid error of naming the atom 01 (zero-one) instead of O1 (o-one). I suspect that this atom is the one which is deleted because recognized as duplicated, but I'm not sure about it and I don't know how to check it. I am sure there are no duplicated atoms in CFY. I feel like this is a fake error message (i.e.: there is an error in my files, but it is not the one that is reported in the message: probably a problem occur around this atom, but it is not exactly ON this atom). However, I am not able to find errors. Hmm that seems weird. Justin's theory sounds plausible, but I haven't seen someone stumble on that before. Also plausible is that pdb2gmx thinks your CFY is a disconnected part of the chain and needs terminating (which might happen with an oxygen named O1?). I stumbled across it when working with the GFP chromophore a while back :) http://redmine.gromacs.org/issues/567 Still technically an open bug, though I agree that it's really expected behavior, provided one knows how pdb2gmx works, which involves lots of steps, of course. -Justin It's possible there's buggy behaviour here that has been fixed in the two years since that code was released. There certainly has been an upgrade of the is this really a new chain machinery. Unless you have a strong scientific reason to keep 4.5.4, I'd switch to 4.6.1 (or 4.5.6 if you really have to keep 4.5). If Justin's fix doesn't work, and you have problems with a more recent version, then we can look closer. BTW the long bond of the other warning message is not involving residue CFY. Yeah, but my bet is those atoms are the C-terminus and N-terminus of the fragments that should form peptide bonds to CFY. Mark Any help is welcome Thank you so much. Anna Il 21.03.2013 12:00 gmx-users-requ...@gromacs.org ha scritto: Dear gmx-users, it's about two weeks that I'm trying to solve this problem, and I can't, so I'm asking your help. I want to do some MD simulations on a protein of the family of green fluorescent protein. This protein, as you know, has a chromophore (CFY) derived from four residues of the protein (F64-C65-Y66-G67) and covalently bound to the rest of the protein chain. How to parametrize this object, since it is not recognized by pdb2gmx? I looked at the gmx-users list and the suggestion was to create a new entry in the .rtp file of the selected forcefield. Indeed, this kind of problem is most easily solved by making a new residue that contains the whole chromophore, such that it links to its neighbours with normal peptide links. -- Message: 5 Date: Thu, 21 Mar 2013 11:46:12 +0100 From: Mark Abraham mark.j.abra...@gmail.com [2] Subject: Re: [gmx-users] help with chromophore of a GFP To: Discussion list for GROMACS users gmx-users@gromacs.org [3] Message-ID: camnumasicymgivb_x5sy1yb44th8vknioqvhzdqq-tam9tn...@mail.gmail.com [4
Re: [gmx-users] help with chromophore of a GFP
I had problems having not used gromacs in years a couple years ago. Try running it through with the output as a pdb from pdb2gmx, cut off all headers, and you can then just compare the two files in gedit emacs or word and see differences. That might help. I routinely just keep everything in pdb format as its easier than jumping back and forth. Original-Nachricht Datum: Thu, 21 Mar 2013 21:43:16 +0100 Von: Mark Abraham mark.j.abra...@gmail.com An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: Re: [gmx-users] help with chromophore of a GFP On Thu, Mar 21, 2013 at 4:30 PM, Anna MARABOTTI amarabo...@unisa.it wrote: Dear Mark, thank you for your message. I'm happy to be on the right track; unfortunately the end point seems to be very far away... I tried to obtain that CFY hydrogens and protein hydrogens are all matching the aminoacids.rtp entry, in order to avoid dealing with aminoacids.hdb. This is what I did: - starting from the pdb file of the protein, I removed CFY entry (prot_noCFY.pdb) - I used pdb2gmx to add H to the protein only: pdb2gmx -f prot_noCFY.pdb -o prot_noCFY_H.pdb -p topol.top - I inserted CFY_H.pdb (obtained with Pymol in a previous passage in which I added H with Pymol to the protein, including CFY) into prot_noCFY_H.pdb, obtaining prot_CFY_H.pdb. In this way, H atoms bound to regular residues have been added using Amber99SB, therefore they are compatible with this ff, and atoms of CFY (previously added with Pymol) have the same naming convention in aminoacids.rtp (that I edited using atom types, charges etc. calculated with Antechamber on this molecule coming from Pymol). Obviously, the atom numbering is not sequential: the last atom of V63 (the last regular residue before CFY) is numbered 938, the first atom of H68 (the first regular residue after CFY) is numbered 939, and the atoms of CFY66 are numbered from 1 to 70. Moreover, since the sequence of atoms in aminoacids.rtp is not the same as in the coordinates of CFY (I adapted the sequence of atoms following the format of other residues in aminoacids.rtp), the numbering of CFY in the prot_CFY_H.pdb is not ordered (1-2-3--69-70) but disordered (19-54-20-55...49-50-24-25). Seems fine. pdb2gmx is mostly about atom/residue naming. grompp is mostly about atom/residue/moleculetype ordering. - At this stage, I used pdb2gmx again to create the topol.top file with all coordinates correct: pdb2gmx -f prot_CFY_H.pdb -o prot_complete.gro -p topol.top (selecting amber99sb forcefield and tip3p for water, as recommended option) This is the message error from pdb2gmx: Read 'FLUORESCENT PROTEIN', 3346 atoms Analyzing pdb file Splitting PDB chains based on TER records or changing chain id. There are 1 chains and 0 blocks of water and 218 residues with 3346 atoms chain #res #atoms 1 'A' 213 3346 I'd be concerned about the difference in residue count here, but 4.5.4 is so old I've no idea whose fault this is. All occupancies are one Opening force field file ./amber99sb.ff/atomtypes.atp Atomtype 1 Reading residue database... (amber99sb) Opening force field file ./amber99sb.ff/aminoacids.rtp Residue 94 Sorting it all out... Opening force field file ./amber99sb.ff/dna.rtp Residue 110 Sorting it all out... Opening force field file ./amber99sb.ff/rna.rtp Residue 126 Sorting it all out... Opening force field file ./amber99sb.ff/aminoacids.hdb Opening force field file ./amber99sb.ff/dna.hdb Opening force field file ./amber99sb.ff/rna.hdb Opening force field file ./amber99sb.ff/aminoacids.n.tdb Opening force field file ./amber99sb.ff/aminoacids.c.tdb Processing chain 1 'A' (3346 atoms, 213 residues) There are 327 donors and 319 acceptors There are 539 hydrogen bonds Will use HISE for residue 22 Will use HISD for residue 38 Will use HISE for residue 62 Will use HISE for residue 68 Will use HISD for residue 109 Will use HISE for residue 119 Will use HISE for residue 172 Will use HISH for residue 193 Will use HISH for residue 197 Will use HISE for residue 217 Identified residue SER3 as a starting terminus. Identified residue SER218 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: MET9 MET11 MET15 HIS22 HIS38 MET41 MET47 SD110 SD149 SD232 NE2317 NE2549 SD596 SD700 MET11 SD149 0.807 MET15 SD232 2.279 1.627 HIS22 NE2317 3.707 2.983 1.466 HIS38 NE2549 1.401 0.928 2.127 3.254 MET41 SD596 1.458 0.665 1.144 2.384 1.001 MET47 SD700 3.059 2.324 0.995 0.801 2.656 1.761 MET53 SD777 2.786 1.999 0.990 1.171 2.160 1.373 0.603 HIS62 NE2917 2.340 1.733 0.833 1.797 1.988 1.236 1.583 HIS68 NE21002 0.884 0.597 1.466 2.916 1.356 0.885 2.347 HIS109 NE21638 2.061 1.886 1.380
[gmx-users] help with chromophore of a GFP
Dear gmx-users, it's about two weeks that I'm trying to solve this problem, and I can't, so I'm asking your help. I want to do some MD simulations on a protein of the family of green fluorescent protein. This protein, as you know, has a chromophore (CFY) derived from four residues of the protein (F64-C65-Y66-G67) and covalently bound to the rest of the protein chain. How to parametrize this object, since it is not recognized by pdb2gmx? I looked at the gmx-users list and the suggestion was to create a new entry in the .rtp file of the selected forcefield. I decided to use Amber99SB since it seemed the better for my scope, then I start trying to parameterize it. This is what I did: * I used Pymol to add H to my pdb file, since I want to use an all H forcefield and since Antechamber (see below) does not work without H * I extracted the segment V63-CFY-H68 from my .pdb file. I did this since, when I extracted CFY only, I had problems with the terminals * Following the Antechamber tutorial, I used Antechamber (using the traditional Amber force field, not GAFF) to calculate charges and to assign atom types to this segment. * I used these calculated parameters in order to add the CFY residue to aminoacids.rtp in amber99sb.ff directory. * I tried to modify also aminoacids.hdb, but since it seemed too complicated to me, I decided to keep it unchanged, and to give pdb2gmx the protein with H already present * No need to add new atom/bond types to ffbonded.itp and ffnonbonded.itp: they seem all present. Since CFY is bound to the rest of protein with common peptide bonds, I did not change specbond.dat either. * I added CFY in residuetypes.dat with the specification Protein In my opinion, all was ready to go, instead... When I launched pdb2gmx to my protein with H added by PyMol, I got immediately an error: Fatal error: Atom H01 in residue SER 3 was not found in rtp entry NSER with 13 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors [1] From this error I understand that: * the code for H in PyMol is different from the code for H in Amber (read from aminoacids.rtp); in order to correct this error, I should add -ignh in order to ignore H in input. * If I add -ignh, all the H of CFY will be ignored too, and I will not be able to add them since I did not modify aminoacids.hdb * since I made calculations on CFY with H added by PyMol, probably also my codes for H will be wrong. * If I use reduce (the Amber tool to add H, as suggested by the tutorial) to add H to my protein, it does not add H to CFY because it complaints that the residue is not in HETATM connection database (but the record CONECT is present in .pdb file). If I add H to CFY alone, I have problems with the terminals. My question is, obviously: how can I parameterize this chromophore correctly? Please give me, if possible, some step-by-step indications on what to do. I made dozens of trials, ALL with errors, and I really do not know how to do. Many thanks in advance and best regards Anna Links: -- [1] http://www.gromacs.org/Documentation/Errors -- 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] help with chromophore of a GFP
On Wed, Mar 20, 2013 at 1:01 PM, Anna MARABOTTI amarabo...@unisa.it wrote: Dear gmx-users, it's about two weeks that I'm trying to solve this problem, and I can't, so I'm asking your help. I want to do some MD simulations on a protein of the family of green fluorescent protein. This protein, as you know, has a chromophore (CFY) derived from four residues of the protein (F64-C65-Y66-G67) and covalently bound to the rest of the protein chain. How to parametrize this object, since it is not recognized by pdb2gmx? I looked at the gmx-users list and the suggestion was to create a new entry in the .rtp file of the selected forcefield. I decided to use Amber99SB since it seemed the better for my scope, then I start trying to parameterize it. This is what I did: * I used Pymol to add H to my pdb file, since I want to use an all H forcefield and since Antechamber (see below) does not work without H * I extracted the segment V63-CFY-H68 from my .pdb file. I did this since, when I extracted CFY only, I had problems with the terminals * Following the Antechamber tutorial, I used Antechamber (using the traditional Amber force field, not GAFF) to calculate charges and to assign atom types to this segment. * I used these calculated parameters in order to add the CFY residue to aminoacids.rtp in amber99sb.ff directory. * I tried to modify also aminoacids.hdb, but since it seemed too complicated to me, I decided to keep it unchanged, and to give pdb2gmx the protein with H already present * No need to add new atom/bond types to ffbonded.itp and ffnonbonded.itp: they seem all present. Since CFY is bound to the rest of protein with common peptide bonds, I did not change specbond.dat either. * I added CFY in residuetypes.dat with the specification Protein In my opinion, all was ready to go, instead... When I launched pdb2gmx to my protein with H added by PyMol, I got immediately an error: Fatal error: Atom H01 in residue SER 3 was not found in rtp entry NSER with 13 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors [1] From this error I understand that: * the code for H in PyMol is different from the code for H in Amber (read from aminoacids.rtp); in order to correct this error, I should add -ignh in order to ignore H in input. * If I add -ignh, all the H of CFY will be ignored too, and I will not be able to add them since I did not modify aminoacids.hdb * since I made calculations on CFY with H added by PyMol, probably also my codes for H will be wrong. * If I use reduce (the Amber tool to add H, as suggested by the tutorial) to add H to my protein, it does not add H to CFY because it complaints that the residue is not in HETATM connection database (but the record CONECT is present in .pdb file). If I add H to CFY alone, I have problems with the terminals. My question is, obviously: how can I parameterize this chromophore correctly? Please give me, if possible, some step-by-step indications on what to do. I made dozens of trials, ALL with errors, and I really do not know how to do. There are parameters published for the GFP chromophore under the CHARMM force field; is there some reason those are unsuitable? No need to reinvent the wheel. With the published parameters, one simply needs to create an .rtp entry and pdb2gmx runs fine, no need to mess with antechamber, PyMOL, etc. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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] help with building DNA in gromacs
Hi Steven I'm running simulations on DNA structures using the amber99sb-ildn FF. I had no problem generating .top and .gro files I might be able to help if you are interested. send me the PDB file. Yocheved On Sun, Jan 20, 2013 at 10:57 PM, Tom dna...@gmail.com wrote: Dear Gromacs User I built DNA with the pdb file and *mol2 But when I used pdb2gmx to obtain *top file, pdb2gmx give error report when I chose charmm27: --- Program pdb2gmx, VERSION 4.5.5 Source code file: resall.c, line: 581 Fatal error: Residue 'T' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Also can not work for the other forcefileds. Why for simple DNA is so difficult to build topology file? Is there any toolbox to help buld the top file? Thanks, Steven -- 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] help with building DNA in gromacs
On 1/20/13 3:57 PM, Tom wrote: Dear Gromacs User I built DNA with the pdb file and *mol2 But when I used pdb2gmx to obtain *top file, pdb2gmx give error report when I chose charmm27: --- Program pdb2gmx, VERSION 4.5.5 Source code file: resall.c, line: 581 Fatal error: Residue 'T' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Also can not work for the other forcefileds. Why for simple DNA is so difficult to build topology file? Your residue names need to match the force field's expectations. That much is true for any molecule passed to pdb2gmx - protein, DNA, RNA, whatever. Consult the .rtp file for your chosen force field and edit your coordinate file accordingly. -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] help with improper angle in gmx
On 1/7/13 6:11 PM, Tom wrote: Dear Gromacs Users I want to use harmonic type of improper angle potential with opls-aa The manu seems not clear. Can anyone give an small example about the format in *rtp file and ffbond.itp file? The names of improper_*_*_*_* tell you to what improper the parameters apply. X, Y, and Z are used to indicate any atom. The only other atoms used are the types that can be used in those positions, i.e. O_C_X_Y is the improper about a carbonyl, while Z_N_X_Y is used in amide groups (peptide bonds). -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
[gmx-users] help about opls-aa for thiophene
Have a look there: http://virtualchemistry.org/molecules/110-02-1/index.php virtualchemistry.org is a really nice site (from David van der Spoel, and others i think), which has many paramters for solvents for the GAFF and OPLS force field. And also Physical properties for these. Greetings Thomas C4H4S. Thiophene is common compound . it seems oplss-aa does not have the parameters for it (such as dihedral angle). Any expert of opls-aa forcefield can help with ff parameters for thiophene? Thanks very much! Steven -- 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] help
On 12/2/12 2:17 AM, 申昊 wrote: Hi everyone， I am a new one on using gromacs. Now I have some problems. [1] I want using g_analyze to calculate the self-ACF with the dist.xvg resulted from g_dist, the file nameddist.xvg consists two lists of time(ns) and distance(nm), respectively. (a)why the result shows a combination of four curves? Is there any options missed (for plotting the only one curve)? The dist.xvg file from g_dist has the total distance, then the x, y, and z components of that distance. If you want only the total distance for analysis, you have to parse that yourself with a script or suitable awk command. (b)I noticed that some regions of the curves were negative, is it correct? Whether the calculation ofACFs is according to the integral methods or cosine methods? You can have negative values within the (x,y,z) portion of dist.xvg since the components are vectors. ACF calculations are discussed in the manual, section 8.5. [2] Does the tetrahedral order parameter of water can be calculated by g_order? How to generate this parameter? g_order is for lipids. [3] Virtual sites are useful in some simulations. I read the tutorial on the web site of http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/. What i really care about is whether the virtual sites should always be used for gas state. I mean, in solutions, the oscillations of the angles are rational. My virtual site tutorial is one example of special uses of virtual sites dealing solely with linear molecules. Virtual sites can be useful in a number of situations. -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
[gmx-users] help
Hi everyone， I am a new one on using gromacs. Now I have some problems. [1] I want using g_analyze to calculate the self-ACF with the dist.xvg resulted from g_dist, the file nameddist.xvg consists two lists of time(ns) and distance(nm), respectively. (a)why the result shows a combination of four curves? Is there any options missed (for plotting the only one curve)? (b)I noticed that some regions of the curves were negative, is it correct? Whether the calculation ofACFs is according to the integral methods or cosine methods? [2] Does the tetrahedral order parameter of water can be calculated by g_order? How to generate this parameter? [3] Virtual sites are useful in some simulations. I read the tutorial on the web site of http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/. What i really care about is whether the virtual sites should always be used for gas state. I mean, in solutions, the oscillations of the angles are rational. Any questions would be greatly appreciated! Thanks. Hao Shen -- 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] help
Please unsubscribe. Thank you. Best, Marlon Am 05.10.2012 12:39, schrieb gmx-users-requ...@gromacs.org: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: regarding g_covar (ran friedman) 2. Re: The No. of the CO2 melecules in top file can not be updated correctly (Justin Lemkul) 3. Re: PME error for energy minimization of TMD in lipidbilayer (Justin Lemkul) 4. Re: Error There is no domain decomposition for 6 nodes that is compatible (Justin Lemkul) 5. Re: Interaction energy calculation.. (Justin Lemkul) 6. Re: Interaction energy calculation.. (rama david) 7. Re: Interaction energy calculation.. (Justin Lemkul) -- Message: 1 Date: Fri, 5 Oct 2012 12:01:31 +0200 From: ran friedmanran.fried...@gmail.com Subject: Re: [gmx-users] regarding g_covar To: gmx-users@gromacs.org Message-ID: cad++iooghk3pe5w6w2ezbwadch8inrozn6xnd6+hakrnipm...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi, Did you try using another structural form (gro or pdb) instead of tpr? The most recent version that I have is for GMX 4.04. I'll send it to you off list. Ran Message: 6 Date: Fri, 5 Oct 2012 11:30:41 +0300 From: R.Vidya Rajendran (10PHD013)vidya2...@vit.ac.in Subject: [gmx-users] regarding g_covar To: gmx-users@gromacs.org Message-ID: CAGqYpqAhDbCmCv=xreoa-7y0buy5odck6aaa_b5qlr7rjw+...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hello Everybody, I am using g_covar with -xpmc flag in-oder to generate matrix of atomic correlation coefficients. At present I am using g_covar script given by Ran, which I downloaded from gromacs user modified script pool. Since Ran's script is for gromacs 3.3.3 and it not accept .trp input from upgraded version (eg 4.5.5). Anybody have upgraded g_covar which can do the same job. regards Vidya -- Message: 2 Date: Fri, 05 Oct 2012 06:05:31 -0400 From: Justin Lemkuljalem...@vt.edu Subject: Re: [gmx-users] The No. of the CO2 melecules in top file can not be updated correctly To: Discussion list for GROMACS usersgmx-users@gromacs.org Message-ID:506eb0eb.8010...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 10/5/12 5:18 AM, Bao Kai wrote: Hi, Justin, Thank you for your reply. It is a little weird and inconvienient that genbox does not update the No. of solute molecules. Is it designed in this way? Does it have any reason for that? The principal function of genbox is to solvate systems, usually with water. The other things it can do are added on, but the code is designed around the most commmon usage. Insertion of molecules is not guaranteed to work, so if a user specifies a number of molecules to add and then genbox cannot, then either it will update with topology with the actual number inserted (which may disagree with the command line, and users may ignore any failures and proceed) or the number requested (which may then fail for the opposite reason). You can see how it becomes a slippery slope to try to make software out-think the user. For my case, the inear, 3-atom model of CO2 works pretty well. I got the model from a paper from Zhenhao Duan. I guess I will use this model for the project before I get something wrong. Good luck. Linear angles are generally not stable. -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] help
On 10/5/12 7:20 AM, Marlon Hinner wrote: Please unsubscribe. Thank you. Per the instructions in the footer of every mail on the list: * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. -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
[gmx-users] help with interaction of type atom in the topology database, but an atom of that name was not found in residue error
Hello Gromacs Users: I apologize for asking a question that has come up several times in the forum, but I have read the answers to those posts and I am not still unable to fix the error based on the suggestions in the previous emails. It is completely possible that I am just not seeing the obvious, so I apologize, but I would welcome any advice. I just have a methylated glycine that I would like to use (SAR) within a peptide with the AMBER force field, but when I try to build the cyclic compound it writes out: Opening force field file ./amber99sb_lipid.ff/atomtypes.atp Atomtype 1 Reading residue database... (amber99sb_lipid) Opening force field file ./amber99sb_lipid.ff/aminoacids.rtp Residue 100 Sorting it all out... Opening force field file ./amber99sb_lipid.ff/aminoacids.hdb Back Off! I just backed up topol.top to ./#topol.top.59# Processing chain 1 'A' (85 atoms, 11 residues) Identified residue ALA1 as a starting terminus. Identified residue ALA11 as a ending terminus. 9 out of 9 lines of specbond.dat converted successfully Opening force field file ./amber99sb_lipid.ff/aminoacids.arn Checking for duplicate atoms --- Program pdb2gmx, VERSION 4.5.5 Source code file: pgutil.c, line: 91 Fatal error: Atom CB is used in an interaction of type atom in the topology database, but an atom of that name was not found in residue number 7. However, my residue 7 should not have a CB atom, I'm not seeing it in my pdb file or the .rtp file (impropers section or otherwise). Perhaps that residue is being skipped, but all of my atoms are ATOM rather than HETATM, and I don't have any tabs messing up the fields. this is the SAR (residue 7) section in my .rtp file [ SAR ] [ atoms ] NN -0.22670 1 CNCT -0.22340 2 HN1H0.10210 3 HN2H0.10210 4 HN3H0.10210 5 CACT -0.02520 6 HA2H1 0.06980 7 HA3H1 0.06980 8 CC0.59730 9 OO -0.5679010 [ bonds ] NCN NCA CA C CA HA2 CA HA3 CN HN1 CN HN2 CN HN3 C O -C N [ impropers ] -CCA N H CA+N C O and here is a chunk of my pdb file MODEL1 ATOM 1 N ALA A 1 -5.608 1.167 2.062 1.000.00 N1+ ATOM 2 CA ALA A 1 -4.930 0.579 3.183 1.00 0.00 C ATOM 3 CB ALA A 1 -5.857 0.458 4.396 1.00 0.00 C ATOM 4 C ALA A 1 -3.814 1.597 3.525 1.00 0.00 C ATOM 5 O ALA A 1 -4.063 2.822 3.391 1.00 0.00 O ATOM 6 N MLE A 2 -2.575 1.132 3.819 1.00 0.00 N ATOM 7 CN MLE A 2 -2.315 -0.257 4.265 1.00 0.00 C ATOM 8 CA MLE A 2 -1.398 2.052 3.941 1.00 0.00 C ATOM 9 CB MLE A 2 -1.091 2.218 5.462 1.00 0.00 C ATOM 10 CG MLE A 2 -2.145 2.883 6.382 1.00 0.00 C ATOM 11 CD1 MLE A 2 -1.689 2.877 7.897 1.00 0.00 C ATOM 12 CD2 MLE A 2 -2.626 4.302 5.946 1.00 0.00 C ATOM 45 N ABA A 6 4.961 4.195 -6.289 1.00 0.00 N ATOM 46 CA ABA A 6 5.219 4.813 -7.615 1.00 0.00 C ATOM 47 CB ABA A 6 6.627 4.541 -8.037 1.00 0.00 C ATOM 48 CG ABA A 6 7.673 5.523 -7.418 1.00 0.00 C ATOM 49 C ABA A 6 4.374 4.037 -8.636 1.00 0.00 C ATOM 50 O ABA A 6 4.360 2.841 -8.453 1.00 0.00 O ATOM 51 N SAR A 7 3.818 4.705 -9.676 1.00 0.00 N ATOM 52 CN SAR A 7 4.087 6.071 -9.873 1.00 0.00 C ATOM 53 CA SAR A 7 2.929 3.969 -10.548 1.00 0.00 C ATOM 54 C SAR A 7 1.449 4.131 -10.258 1.00 0.00 C ATOM 55 O SAR A 7 0.975 5.236 -10.559 1.00 0.00 O ATOM 56 N MLE A 8 0.814 3.165 -9.517 1.00 0.00 N ATOM 57 CN MLE A 8 1.365 1.822 -9.318 1.00 0.00 C ATOM 58 CA MLE A 8-0.491 3.432 -8.917 1.00 0.00 C ATOM 59 CB MLE A 8-1.599 2.488 -9.538 1.00 0.00 C ATOM 60 CG MLE A 8-2.739 3.173 -10.337 1.00 0.00 C ATOM 61 CD1 MLE A 8-3.758 3.767 -9.396 1.00 0.00 C ATOM 62 CD2 MLE A 8-2.404
Re: [gmx-users] help with interaction of type atom in the topology database, but an atom of that name was not found in residue error
On 8/30/12 9:23 PM, Katrina Lexa wrote: Hello Gromacs Users: I apologize for asking a question that has come up several times in the forum, but I have read the answers to those posts and I am not still unable to fix the error based on the suggestions in the previous emails. It is completely possible that I am just not seeing the obvious, so I apologize, but I would welcome any advice. I just have a methylated glycine that I would like to use (SAR) within a peptide with the AMBER force field, but when I try to build the cyclic compound it writes out: Opening force field file ./amber99sb_lipid.ff/atomtypes.atp Atomtype 1 Reading residue database... (amber99sb_lipid) Opening force field file ./amber99sb_lipid.ff/aminoacids.rtp Residue 100 Sorting it all out... Opening force field file ./amber99sb_lipid.ff/aminoacids.hdb Back Off! I just backed up topol.top to ./#topol.top.59# Processing chain 1 'A' (85 atoms, 11 residues) Identified residue ALA1 as a starting terminus. Identified residue ALA11 as a ending terminus. 9 out of 9 lines of specbond.dat converted successfully Opening force field file ./amber99sb_lipid.ff/aminoacids.arn Checking for duplicate atoms --- Program pdb2gmx, VERSION 4.5.5 Source code file: pgutil.c, line: 91 Fatal error: Atom CB is used in an interaction of type atom in the topology database, but an atom of that name was not found in residue number 7. However, my residue 7 should not have a CB atom, I'm not seeing it in my pdb file or the .rtp file (impropers section or otherwise). Perhaps that residue is being skipped, but all of my atoms are ATOM rather than HETATM, and I don't have any tabs messing up the fields. this is the SAR (residue 7) section in my .rtp file [ SAR ] [ atoms ] NN -0.22670 1 CNCT -0.22340 2 HN1H0.10210 3 HN2H0.10210 4 HN3H0.10210 5 CACT -0.02520 6 HA2H1 0.06980 7 HA3H1 0.06980 8 CC0.59730 9 OO -0.5679010 [ bonds ] NCN NCA CA C CA HA2 CA HA3 CN HN1 CN HN2 CN HN3 C O -C N [ impropers ] -CCA N H CA+N C O and here is a chunk of my pdb file MODEL1 ATOM 1 N ALA A 1 -5.608 1.167 2.062 1.000.00 N1+ ATOM 2 CA ALA A 1 -4.930 0.579 3.183 1.00 0.00 C ATOM 3 CB ALA A 1 -5.857 0.458 4.396 1.00 0.00 C ATOM 4 C ALA A 1 -3.814 1.597 3.525 1.00 0.00 C ATOM 5 O ALA A 1 -4.063 2.822 3.391 1.00 0.00 O ATOM 6 N MLE A 2 -2.575 1.132 3.819 1.00 0.00 N ATOM 7 CN MLE A 2 -2.315 -0.257 4.265 1.00 0.00 C ATOM 8 CA MLE A 2 -1.398 2.052 3.941 1.00 0.00 C ATOM 9 CB MLE A 2 -1.091 2.218 5.462 1.00 0.00 C ATOM 10 CG MLE A 2 -2.145 2.883 6.382 1.00 0.00 C ATOM 11 CD1 MLE A 2 -1.689 2.877 7.897 1.00 0.00 C ATOM 12 CD2 MLE A 2 -2.626 4.302 5.946 1.00 0.00 C ATOM 45 N ABA A 6 4.961 4.195 -6.289 1.00 0.00 N ATOM 46 CA ABA A 6 5.219 4.813 -7.615 1.00 0.00 C ATOM 47 CB ABA A 6 6.627 4.541 -8.037 1.00 0.00 C ATOM 48 CG ABA A 6 7.673 5.523 -7.418 1.00 0.00 C ATOM 49 C ABA A 6 4.374 4.037 -8.636 1.00 0.00 C ATOM 50 O ABA A 6 4.360 2.841 -8.453 1.00 0.00 O ATOM 51 N SAR A 7 3.818 4.705 -9.676 1.00 0.00 N ATOM 52 CN SAR A 7 4.087 6.071 -9.873 1.00 0.00 C ATOM 53 CA SAR A 7 2.929 3.969 -10.548 1.00 0.00 C ATOM 54 C SAR A 7 1.449 4.131 -10.258 1.00 0.00 C ATOM 55 O SAR A 7 0.975 5.236 -10.559 1.00 0.00 O ATOM 56 N MLE A 8 0.814 3.165 -9.517 1.00 0.00 N ATOM 57 CN MLE A 8 1.365 1.822 -9.318 1.00 0.00 C ATOM 58 CA MLE A 8-0.491 3.432 -8.917 1.00 0.00 C ATOM 59 CB MLE A 8-1.599 2.488 -9.538 1.00 0.00 C ATOM 60 CG MLE A 8-2.739 3.173 -10.337 1.00 0.00
[gmx-users] Help of mdrun-gpu
Dear All, I just configured the mdrun-gpu. When I tested mdrun-gpu by running gromacs-gpubench-dhfr.tar.gz which is from gromacs website. Unfortunately, it failed with segmentation fault. I don't think the system has any equilibrium problem since it works fine in mdrun. I will appreciate a lot if anyone could help me for it. Best Wishes, Jiangfeng. Jiangfeng Du, PhD Student Cardiovascular Research Institute Maastricht Department of Biochemistry P.O. Box 616 Mobile: +31-681741859 FAX: +31-43-3884159 6200 MD Maastricht The Netherlands-- 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
Re: [gmx-users] Help of mdrun-gpu
On 28/07/2012 12:58 AM, Du Jiangfeng (BIOCH) wrote: Dear All, I just configured the mdrun-gpu. When I tested mdrun-gpu by running gromacs-gpubench-dhfr.tar.gz which is from gromacs website. Unfortunately, it failed with segmentation fault. I don't think the system has any equilibrium problem since it works fine in mdrun. I will appreciate a lot if anyone could help me for it. Best Wishes, Jiangfeng. Have you read the available documentation? Do you have a supported GPU? Mark -- 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
[gmx-users] help!!
i am using the tutorial KALP15 in DPPC for my protein in bilipid membrane SIMULATION. i have reached Step Three: Defining the Unit Cell Adding Solvent where i hav to pack the lipids around the protein using InflateGro. how do i start using inflategro? my last step was : to generate this new position restraint file using genrestr: genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 10 After which ,In the .mdp file used for the minimizations, i added a line define = -DSTRONG_POSRES to make use of these new position restraints. when i next gave the command :perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat ERROR Can't open perl script inflategro.pl: No such file or directory WHAT SHOULD I DO??? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] help!!
On 6/15/12 5:58 AM, ankita oindrila wrote: i am using the tutorial KALP15 in DPPC for my protein in bilipid membrane SIMULATION. i have reached Step Three: Defining the Unit Cell Adding Solvent where i hav to pack the lipids around the protein using InflateGro. how do i start using inflategro? my last step was : to generate this new position restraint file using genrestr: genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 10 After which ,In the .mdp file used for the minimizations, i added a line define = -DSTRONG_POSRES to make use of these new position restraints. when i next gave the command :perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat ERROR Can't open perl script inflategro.pl: No such file or directory WHAT SHOULD I DO??? Download the script from the link provided in the tutorial. -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] Help with free energy
Hi Milinda, There are different methods to do Free energy. I am using Thermodynamics Integration method; hence if you are interested to use TI I am willing to guide you, but I never use bar method. I did some parametrization so if you float your topology and mpd files I will give you some idea how to do it. Cheers, Emmanuel From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Saturday, May 05, 2012 12:59 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Help with free energy Please keep all correspondence on the gmx-users list. I am not a private tutor and you have better odds of solving your problem by allowing others to provide input. On 5/4/12 8:01 PM, Milinda Samaraweera wrote: Hi Justin Im a very new to using Gromacs. I tried to reproduce the values in shirts paper for methane. And using a similar model for study the hydration of Anilinium. If I send you my input files could you please take a look and give me some suggestions. Were you able to reproduce the methane hydration value? Aniline and anilinium are different, with the latter being more difficult to deal with on account of its charge. If you post your topology, perhaps someone will have some tips on how to modify it to produce better results, but proper small molecule parameterization is not a task well-suited for new users. It may take considerable time and effort to derive a high-quality topology. For general advice, consult: http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 -- 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] Help with free energy
Hi Im trying to calculate the hydration free energy for the molecule Aniline And I get a free energy value about 10 kcal higher than the experimental value What I do is I couple vdw then charges from a dummy state and add the two delta G values using the g_bar method. If you have any idea why is this so Please send me an e-mail thanks Milinda Samaraweera University of Connecticut Department of Chemistry 55 N Eagleville road unit 3060 Storrs CT USA-- 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] Help with free energy
On 5/4/12 3:56 PM, Milinda Samaraweera wrote: Hi Im trying to calculate the hydration free energy for the molecule Aniline And I get a free energy value about 10 kcal higher than the experimental value What I do is I couple vdw then charges from a dummy state and add the two delta G values using the g_bar method. If you have any idea why is this so Please send me an e-mail If the parameters do not produce observables that reflect reality (provided the error bars give you confidence in the value), you need a better model and thus a better topology. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] Help with free energy
Please keep all correspondence on the gmx-users list. I am not a private tutor and you have better odds of solving your problem by allowing others to provide input. On 5/4/12 8:01 PM, Milinda Samaraweera wrote: Hi Justin Im a very new to using Gromacs. I tried to reproduce the values in shirts paper for methane. And using a similar model for study the hydration of Anilinium. If I send you my input files could you please take a look and give me some suggestions. Were you able to reproduce the methane hydration value? Aniline and anilinium are different, with the latter being more difficult to deal with on account of its charge. If you post your topology, perhaps someone will have some tips on how to modify it to produce better results, but proper small molecule parameterization is not a task well-suited for new users. It may take considerable time and effort to derive a high-quality topology. For general advice, consult: http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
[gmx-users] help about Inconsistent DD boundary staggering limits
Hi Guys, I have done the simulation. The total steps is 500. At around 90 steps, the error information appear like the followings. Please give me some suggestions to fix it. Best wishes, Desheng -- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 102, will try to stop all the nodes Halting parallel program mdrun on CPU 102 out of 120 Error on node 105, will try to stop all the nodes Halting parallel program mdrun on CPU 105 out of 120 Error on node 51, will try to stop all the nodes Halting parallel program mdrun on CPU 51 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 81, will try to stop all the nodes Halting parallel program mdrun on CPU 81 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 63, will try to stop all the nodes Halting parallel program mdrun on CPU 63 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 33, will try to stop all the nodes Halting parallel program mdrun on CPU 33 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 54, will try to stop all the nodes Halting parallel program mdrun on CPU 54 out of 120 Error on node 24, will try to stop all the nodes Halting parallel program mdrun on CPU 24 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 84, will try to stop all the nodes Halting parallel program mdrun on CPU 84 out of 120 gcq#359: If it weren't for bad luck, we'd have no luck at all (The Unthanks) gcq#359: If it weren't for bad luck, we'd have no luck at all (The Unthanks) application called MPI_Abort(MPI_COMM_WORLD, -1) - process 42
Re: [gmx-users] help about Inconsistent DD boundary staggering limits
On 4/26/12 2:52 PM, Desheng Zheng wrote: Hi Guys, I have done the simulation. The total steps is 500. At around 90 steps, the error information appear like the followings. Please give me some suggestions to fix it. Based on the comment that precedes the error call in the code: /* Make sure that the grid is not shifted too much */ I would assume that this means your system has simply become unstable and is blowing up. http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin Best wishes, Desheng -- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 102, will try to stop all the nodes Halting parallel program mdrun on CPU 102 out of 120 Error on node 105, will try to stop all the nodes Halting parallel program mdrun on CPU 105 out of 120 Error on node 51, will try to stop all the nodes Halting parallel program mdrun on CPU 51 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 81, will try to stop all the nodes Halting parallel program mdrun on CPU 81 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 63, will try to stop all the nodes Halting parallel program mdrun on CPU 63 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 33, will try to stop all the nodes Halting parallel program mdrun on CPU 33 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 54, will try to stop all the nodes Halting parallel program mdrun on CPU 54 out of 120 Error on node 24, will try to stop all the nodes Halting parallel program mdrun on CPU 24 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The
Re: [gmx-users] help about Inconsistent DD boundary staggering limits
On 4/26/12 3:30 PM, Desheng Zheng wrote: Thanks Justin! about the Software inconsistency error: Inconsistent DD boundary staggering limits! I still have three concerts. 1. Is it ok, if i use grompp to generate the edr file in gromacs 4.5.5 environmentwith the gro file and top file which were builed under Gromacs 4.0.7 ? Coordinate files and topologies are largely independent of version. There was a reorganization of the force fields between 4.0.7 and 4.5, but you can easily work around such things. 2. In my protein-DPPC lipid membrane, I use the electric filed Ez is 0.3V/nm. whether is the value too high to induce the bowling up? I don't know. The easiest way to deduce the source of the problem is to do so scientifically. Turn off the electric field, does the simulation run? Eliminate other factors systematically until you arrive at the root of the problem. 3. why do the generated edr file in gromacs 4.5.5 environment larger than the edr file in gromacs 4.0.7 environment, even with the same gro file and top file and the same commands? There have been changes to the .edr format and its contents to allow for more features. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] help about Inconsistent DD boundary staggering limits
Thanks Justin! about the Software inconsistency error: Inconsistent DD boundary staggering limits! I still have three concerts. 1. Is it ok, if i use grompp to generate the edr file in gromacs 4.5.5 environmentwith the gro file and top file which were builed under Gromacs 4.0.7 ? 2. In my protein-DPPC lipid membrane, I use the electric filed Ez is 0.3V/nm. whether is the value too high to induce the bowling up? 3. why do the generated edr file in gromacs 4.5.5 environment larger than the edr file in gromacs 4.0.7 environment, even with the same gro file and top file and the same commands? Best wishes, Desheng From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Thursday, April 26, 2012 3:05 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] help about Inconsistent DD boundary staggering limits On 4/26/12 2:52 PM, Desheng Zheng wrote: Hi Guys, I have done the simulation. The total steps is 500. At around 90 steps, the error information appear like the followings. Please give me some suggestions to fix it. Based on the comment that precedes the error call in the code: /* Make sure that the grid is not shifted too much */ I would assume that this means your system has simply become unstable and is blowing up. http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin Best wishes, Desheng -- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 102, will try to stop all the nodes Halting parallel program mdrun on CPU 102 out of 120 Error on node 105, will try to stop all the nodes Halting parallel program mdrun on CPU 105 out of 120 Error on node 51, will try to stop all the nodes Halting parallel program mdrun on CPU 51 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 81, will try to stop all the nodes Halting parallel program mdrun on CPU 81 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 63, will try to stop all the nodes Halting parallel program mdrun on CPU 63 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 33, will try to stop all the nodes Halting parallel program mdrun on CPU 33 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) --- Program mdrun, VERSION
[gmx-users] Help: Anyone worked with Wall?
Dear all, I'm trying to simulate with pbc=xy and I need two walls. My settings are as follows: pbc = xy nwall = 2 wall_atomtype = C C wall_type = 9-3 wall_r_linpot = -1 -1 wall_density= 20 20 wall_ewald_zfac = 3 The problem is how to define wall_atomtype in my topology file (top/itp)? A want to have this solid carbon wall with 9-3 potential. Where in my top/itp file can I define such atoms? This is my top file: #include ffG53a6.itp #include spc.itp [ system ] Pure Water with walls [ molecules ] SOL216 When I gmxdump the generated tpr file, I saw no C atoms are defined; and it showed: wall_atomtype[0] = 2 wall_atomtype[1] = 2 which corresponds to the hydrogen atom in my top file. And according to my forcefield, the LJ parameters for H is 0,0. So there is basically no wall. When I tried to simulate with this setting, the water molecules went out of the box (in z direction) and moved far away. And according to g_energy, there is no interaction energy between water and wall. So there indeed is no wall. Can you help me with defining wall atom? If you have already finished any tasks with this wall algorithm, can you kindly attach your topology files to me? Soo many thanks! -- Huaichen(Bobby) ZHANG +31 648478172 MSc Sustainable Energy Engineering Royal Institute of Technology (Sweden) Eindhoven University of Technology (Netherland) -- 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] Help: Anyone worked with Wall?
For walls, the atoms in the wall are virtual. Remember that 9-3 LJ integratees over the volume behind the wall so you will have to set your atom density appropriately. Setting wall_density to 20/nm^3 for 9-3 wall leads to 20 carbon atoms per nm^3. That's not going to be totally solid, imo. I am using 10-4 2-D walls to effect here: nwall = 2 wall_type = 10-4 wall_density = 5 5 wall_atomtype = CG331 CG331 wall_r_linpot = -1 wall_ewald_zfac = 3 ewald_geometry=3dc pbc=xy (CG331 is just a methyl group carbon specific to my forcefield). On 2012-04-05 10:08:02PM +0200, Huaichen(Bobby) Zhang wrote: Dear all, I'm trying to simulate with pbc=xy and I need two walls. My settings are as follows: pbc = xy nwall = 2 wall_atomtype = C C wall_type = 9-3 wall_r_linpot = -1 -1 wall_density= 20 20 wall_ewald_zfac = 3 The problem is how to define wall_atomtype in my topology file (top/itp)? A want to have this solid carbon wall with 9-3 potential. Where in my top/itp file can I define such atoms? This is my top file: #include ffG53a6.itp #include spc.itp [ system ] Pure Water with walls [ molecules ] SOL216 When I gmxdump the generated tpr file, I saw no C atoms are defined; and it showed: wall_atomtype[0] = 2 wall_atomtype[1] = 2 which corresponds to the hydrogen atom in my top file. And according to my forcefield, the LJ parameters for H is 0,0. So there is basically no wall. When I tried to simulate with this setting, the water molecules went out of the box (in z direction) and moved far away. And according to g_energy, there is no interaction energy between water and wall. So there indeed is no wall. Can you help me with defining wall atom? If you have already finished any tasks with this wall algorithm, can you kindly attach your topology files to me? Soo many thanks! -- Huaichen(Bobby) ZHANG +31 648478172 MSc Sustainable Energy Engineering Royal Institute of Technology (Sweden) Eindhoven University of Technology (Netherland) -- 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] help needed
*SIMULATION OF LYSOZYME IN WATER USING GROMACS-4.0.5 * STEP: TO NEUTRALIZE THE +8 CHARGE WITH 8 CL- MOLECULES* COMMAND GIVEN : [root@localhost gromacs-4.0.5]# genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -nn 8* :-) G R O M A C S (-: GRoups of Organic Molecules in ACtion for Science :-) VERSION 4.0.5 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) genion (-: Option Filename Type Description -s ions.tpr InputRun input file: tpr tpb tpa -tabletable.xvg Input, Opt. xvgr/xmgr file -n index.ndx Input, Opt. Index file -o 1AKI_solv_ions.gro Output Structure file: gro g96 pdb -g genion.log Output Log file -potpot.pdb Output, Opt. Protein data bank file -p topol.top In/Out, Opt! Topology file Option Type Value Description -- -[no]h bool no Print help info and quit -niceint19 Set the nicelevel -[no]xvgrbool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -np int0 Number of positive ions -pname string NA Name of the positive ion -pq int1 Charge of the positive ion -nn int8 Number of negative ions -nname string CL Name of the negative ion -nq int-1 Charge of the negative ion -rminreal 0.6 Minimum distance between ions -[no]random bool yes Use random placement of ions instead of based on potential. The rmin option should still work -seedint1993Seed for random number generator -scale real 0.001 Scaling factor for the potential for -pot -concreal 0 Specify salt concentration (mol/liter). This will add sufficient ions to reach up to the specified concentration as computed from the volume of the cell in the input tpr file. Overrides the -np and nn options. -[no]neutral bool no This option will add enough ions to neutralize the system. In combination with the concentration option a neutral system at a given salt concentration will be generated. WARNING: turning of free energy, will use lambda=0 Reading file ions.tpr, VERSION 4.0.5 (single precision) Using a coulomb cut-off of 1 nm Will try to add 0 NA ions and 8 CL ions. Select a continuous group of solvent molecules Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Group 0 ( System) has 39055 elements Group 1 ( Protein) has 1960 elements Group 2 ( Protein-H) has 1001 elements Group 3 ( C-alpha) has 129 elements Group 4 (Backbone) has 387 elements Group 5 ( MainChain) has 517 elements Group 6 (MainChain+Cb) has 634 elements Group 7 ( MainChain+H) has 646 elements Group 8 ( SideChain) has 1314 elements Group 9 ( SideChain-H) has 484 elements Group10 ( Prot-Masses) has 1960 elements Group11 ( Non-Protein) has 37095 elements Group12 ( SOL) has 37095 elements Group13 ( Other) has 37095 elements Select a group: 12 Selected 12: 'SOL' Number of (3-atomic) solvent molecules: 12365 Processing topology Replacing 12357 solute molecules in topology file (topol.top) by 0 NA and 8 CL ions. Back Off! I just backed up topol.top to ./#topol.top.2# Replacing solvent molecule 1450 (atom 6310) with CL Replacing solvent molecule 9368 (atom 30064) with CL Replacing solvent molecule 6035 (atom 20065) with CL Replacing solvent molecule 10461 (atom 33343) with CL Replacing solvent molecule 4117 (atom 14311) with CL Replacing solvent molecule 1980 (atom 7900) with CL Replacing solvent molecule 4774 (atom 16282) with CL Replacing solvent molecule 10956 (atom 34828) with CL *THE PROBLEM FACED IS*: THE REPLACED CL MOLECULES CANNOT BE SEEN IN THE UPDATED TOPOLOGY FILE. PLEASE TELL ME HOW TO ANALYSE IT. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please
Re: [gmx-users] help needed
On 31/03/2012 6:02 PM, oindrila das wrote: *SIMULATION OF LYSOZYME IN WATER USING GROMACS-4.0.5 * STEP: TO NEUTRALIZE THE +8 CHARGE WITH 8 CL- MOLECULES* COMMAND GIVEN : [root@localhost gromacs-4.0.5]# genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -nn 8* :-) G R O M A C S (-: GRoups of Organic Molecules in ACtion for Science :-) VERSION 4.0.5 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org http://www.gromacs.org/ for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) genion (-: Option Filename Type Description -s ions.tpr InputRun input file: tpr tpb tpa -tabletable.xvg Input, Opt. xvgr/xmgr file -n index.ndx Input, Opt. Index file -o 1AKI_solv_ions.gro Output Structure file: gro g96 pdb -g genion.log Output Log file -potpot.pdb Output, Opt. Protein data bank file -p topol.top In/Out, Opt! Topology file Option Type Value Description -- -[no]h bool no Print help info and quit -niceint19 Set the nicelevel -[no]xvgrbool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -np int0 Number of positive ions -pname string NA Name of the positive ion -pq int1 Charge of the positive ion -nn int8 Number of negative ions -nname string CL Name of the negative ion -nq int-1 Charge of the negative ion -rminreal 0.6 Minimum distance between ions -[no]random bool yes Use random placement of ions instead of based on potential. The rmin option should still work -seedint1993Seed for random number generator -scale real 0.001 Scaling factor for the potential for -pot -concreal 0 Specify salt concentration (mol/liter). This will add sufficient ions to reach up to the specified concentration as computed from the volume of the cell in the input tpr file. Overrides the -np and nn options. -[no]neutral bool no This option will add enough ions to neutralize the system. In combination with the concentration option a neutral system at a given salt concentration will be generated. WARNING: turning of free energy, will use lambda=0 Reading file ions.tpr, VERSION 4.0.5 (single precision) Using a coulomb cut-off of 1 nm Will try to add 0 NA ions and 8 CL ions. Select a continuous group of solvent molecules Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Group 0 ( System) has 39055 elements Group 1 ( Protein) has 1960 elements Group 2 ( Protein-H) has 1001 elements Group 3 ( C-alpha) has 129 elements Group 4 (Backbone) has 387 elements Group 5 ( MainChain) has 517 elements Group 6 (MainChain+Cb) has 634 elements Group 7 ( MainChain+H) has 646 elements Group 8 ( SideChain) has 1314 elements Group 9 ( SideChain-H) has 484 elements Group10 ( Prot-Masses) has 1960 elements Group11 ( Non-Protein) has 37095 elements Group12 ( SOL) has 37095 elements Group13 ( Other) has 37095 elements Select a group: 12 Selected 12: 'SOL' Number of (3-atomic) solvent molecules: 12365 Processing topology Replacing 12357 solute molecules in topology file (topol.top) by 0 NA and 8 CL ions. Back Off! I just backed up topol.top to ./#topol.top.2# Replacing solvent molecule 1450 (atom 6310) with CL Replacing solvent molecule 9368 (atom 30064) with CL Replacing solvent molecule 6035 (atom 20065) with CL Replacing solvent molecule 10461 (atom 33343) with CL Replacing solvent molecule 4117 (atom 14311) with CL Replacing solvent molecule 1980 (atom 7900) with CL Replacing solvent molecule 4774 (atom 16282) with CL Replacing solvent molecule 10956 (atom 34828) with CL _THE PROBLEM FACED IS_: THE REPLACED CL MOLECULES CANNOT BE SEEN IN THE UPDATED TOPOLOGY FILE. PLEASE TELL ME HOW TO ANALYSE IT. What do you mean by
Re: [gmx-users] Help regarding running DSSP in gmx
Hi Chandran, What did you try, and what error did it come up with? What platform are you using, and which version of DSSP? The latest version of DSSP won't work with Gromacs yet. Cheers, Tsjerk On Mon, Mar 19, 2012 at 2:39 PM, chandran karunakaran ckaru2...@yahoo.com wrote: Dear ALL, We could not run DSSP for analysing the secondary structure. Any help in this regard is very much appreciated ***+ Dr.Karunakaran Chandran + Biophysics Department + Medical College of Wisconsin + Milwaukee, WI-53226 + Resi.: 414-443-0085 + Off : 414-456-4034 + From: gmx-users-requ...@gromacs.org gmx-users-requ...@gromacs.org To: gmx-users@gromacs.org Sent: Monday, 19 March 2012 4:30 PM Subject: gmx-users Digest, Vol 95, Issue 125 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Editing potential parameters (Asaf Farhi) 2. nrexcl in topology (Lara Bunte) 3. extending simulation (priya thiyagarajan) 4. Re: nrexcl in topology (R.Perez Garcia) 5. Re: Force constant - Umbrella Sampling (lloyd riggs) -- Message: 1 Date: Mon, 19 Mar 2012 10:06:47 + From: Asaf Farhi asaf.fa...@weizmann.ac.il Subject: [gmx-users] Editing potential parameters To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: 7D02BCA1E8377E4AABC2E8F59B6D0CDA09E25B@IBWMBX01 Content-Type: text/plain; charset=iso-8859-1 Dear Gromacs user Hi. My name is Asaf and I'm trying to edit potential parameters for the non bonded interaction potential terms between specific atoms (k1 for 1 subset of pairs and k2 for anoother subset of pairs). Is the pairs section in the topology file the correct place to do this? and if so how would you incorporate spring constant for particular pair interaction? Many thanks. Best regards, Asaf -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20120319/6adac179/attachment-0001.html -- Message: 2 Date: Mon, 19 Mar 2012 10:19:22 + (GMT) From: Lara Bunte lara.bu...@yahoo.de Subject: [gmx-users] nrexcl in topology To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: 1332152362.73030.yahoomail...@web29401.mail.ird.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Hi in a topology file in the section [ moleculetypes ] is standing ; nrexcl 3 What do this mean? Thanks for help Greetings Lara -- Message: 3 Date: Mon, 19 Mar 2012 03:26:55 -0700 From: priya thiyagarajan priya.thiyagaraja...@gmail.com Subject: [gmx-users] extending simulation To: gmx-users@gromacs.org Message-ID: caeuvtxairnq6ndxppkgg_s34ufzyzvg2z2-bkoaucnqok4f...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 hello sir,, initially i did my simulation for 10ns.. after getting result i analysed it and thought of extending the simulation for another 10ns.. i used following commands.. tpbconv *-s md.tpr -o newmd.tpr -extend 1.00* *mdrun -s newmd.tpr -o md3_2.trr -c md_2.gro -e md_2.edr -g md_2.log -cpi state1.cpt -noappend* is it correct.. we ll use tpbconv to extend the simulation which terminated in the middle.. is it correct to use the same command for completed run... please help me with your answer.. Thanking you sir, -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20120319/9248f3aa/attachment-0001.html -- Message: 4 Date: Mon, 19 Mar 2012 11:27:43 +0100 From: R.Perez Garcia r.perez.gar...@student.rug.nl Subject: Re: [gmx-users] nrexcl in topology To: Lara Bunte lara.bu...@yahoo.de, gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: 7630868d774ff.4f671...@rug.nl Content-Type: text/plain; charset=iso-8859-1 http://lists.gromacs.org/pipermail/gmx-users/2011-May/061072.html On 19-03-12, Lara Bunte lara.bu...@yahoo.de wrote: Hi in a topology file in the section [ moleculetypes ] is standing ; nrexcl 3 What do this mean? Thanks for help Greetings Lara -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the
Re: [gmx-users] Help regarding running DSSP in gmx
On 20/03/2012 12:39 AM, chandran karunakaran wrote: Dear ALL, We could not run DSSP for analysing the secondary structure. Any help in this regard is very much appreciated ***+ Dr.Karunakaran Chandran + Biophysics Department + Medical College of Wisconsin + Milwaukee, WI-53226 + Resi.: 414-443-0085 + Off : 414-456-4034 + You're doing something wrong :-) Please consider and follow the advice here http://www.gromacs.org/Support and ask again. 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] help on replica exchange dynamics with gromacs
Dear friends Can someone help me with tutorial on replica exchange dynamics Thanks in advance Raghuvir -- 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] help on replica exchange dynamics with gromacs
On 13/03/2012 3:17 PM, Raghuvir Pissurlenkar wrote: Dear friends Can someone help me with tutorial on replica exchange dynamics Thanks in advance Raghuvir Search the GROMACS webpage, please. You will want to do some normal tutorials to understand normal workflows first. 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] Help us steer future GROMACS development, with a chance to win a $2000+ Tesla C2075 GPU
Hi everybody! I have a small favor to ask that should hopefully help both us and you in the long run. As some of you might know, we have been working quite closely with NVIDIA for a while to develop a better (and parallel) GPU version of GROMACS to significantly accelerate simulations. With the new Cray XK6 machines including NVIDIA GPUs, this is likely to become tremendously important for supercomputers in general too. An important part of this project has been the discussions about what type of simulations are most important to improve in the future. Is it single long trajectories? Performance for small systems? Parallelization for large systems? Extreme throughput? Statistical modeling? Of course we have our own applications, but from the usage point-of-view we are just one user group out of many, and when NVIDIA asked us whether we would be interested in a survey we figured this would be a great way to actually determine what is most important for the entire community rather than just keep guessing. To tell the truth, we know very little about your specific needs, but this is your chance to change that and influence not only the next version, but the future 5-10 years of GROMACS development efforts, and specifically speed up _your_ type of simulations on all types of hardware. We would be extremely grateful if you could spare 10 minutes of your time and participate in this GROMACS survey, and we would appreciate it if you encourage your colleagues and other GROMACS users to do the same. They don't need to be users of the GROMACS GPU code, just general users. https://www.surveymonkey.com/s/YD9ZMJK Thanks a lot for your help! Mark Berger and his colleagues at NVIDIA have been exceptionally supportive, and since they are also interested in the results they have generously donated two fancy workstation-class C2075 Tesla GPUs. Everyone who completes the survey will be entered into a free drawing, where two winners will each receive one of these cards. I will announce the winners here in a few weeks after we close the survey. This could be a great way to kickstart your GPU simulation usage! Nvidia sweepstake rules: http://www.nvidia.com/object/sweepstakes-official-rules.html All the best, Erik Lindahl The GROMACS Development team -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] help with ed sampling
Hi everybody, I am trying to do essential dynamics sampling from a starting structure to the target structure, so I am using the command: make_edi_d -f ../eigenvec.trr -eig ../eigenval.xvg -s topol.tpr -radcon 1 -n index.ndx -tar target.gro The projection of the starting structure and of the target structure on the first eigenvector is 3.5 and -2.8, respectively (I double checked the projection of these structures on the first eigenvector). However, the sam.edo shows that after about 5000 steps the sampling is constrained at a value of the projection of 2.4 and the contracting radius becomes 0 (the initial value of the contracting radius is 1.1). If I give two first eigenvectors instead of the first one: make_edi_d -f ../eigenvec.trr -eig ../eigenval.xvg -s topol.tpr -radcon 1-2 -n index.ndx -tar target.gro in the sam.edo file the contracting radius starts from 2.2 and the sampling stops at the same point as before. I do not understand. Can I chose the initial value of the contracting radius? Why does not the sampling continue up to the target's projection value? Thanks in advance, Neva -- 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] Help about g_hbond and angle cutoff
Hi gromacs Users: I have a doubt respect to how g_hbond consider the cutoff angle (-a) Acceptor-Donnor-Hydrogen in gromacs 4.5.4. I need to evaluate the hydrogen bonds with an anble larger than 135°. The default value of the angle is cutoff in g_hbond is 30°, so this value means that the H. bonds larger than 30° will be evaluated? or the angles to evaluate will be larger than 150° (180° - 30°) as is proposed in this post for gromacs 3.1.1: http://lists.gromacs.org/pipermail/gmx-users/2003-January/003970.html If the second case was correct, then the value to use in my case should be -a 45 for looking all H. bonds larger than 135°? Thank you, bye. -- 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] Help about g_hbond and angle cutoff
alejandro esteban blanco munoz wrote: Hi gromacs Users: I have a doubt respect to how g_hbond consider the cutoff angle (-a) Acceptor-Donnor-Hydrogen in gromacs 4.5.4. I need to evaluate the hydrogen bonds with an anble larger than 135°. The default value of the angle is cutoff in g_hbond is 30°, so this value means that the H. bonds larger than 30° will be evaluated? or the angles to evaluate will be larger than 150° (180° - 30°) as is proposed in this post for gromacs 3.1.1: http://lists.gromacs.org/pipermail/gmx-users/2003-January/003970.html If the second case was correct, then the value to use in my case should be -a 45 for looking all H. bonds larger than 135°? Yes, note the order of the terms. The default value of 30 degrees corresponds to the A-D-H angle, so that would make the D-H-A value (which is I think what you are considering) 150 degrees in the default case. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] Help with non-standard residues and molecular structures
On 4/01/2012 4:57 PM, Robert Hamers wrote: I'd appreciate any help -- I'm trying to model a small (~ 20-carbon ) molecule linked to a diamond surface. I got the diamond surface with 1500 atoms working fine all the way through to the MD simulation and it looks great. But I'm getting stuck on the molecule, which is not a protein but a moderately short-chain molecule that has a triazole (N3C2) in the middle of it. I thought in order to make this work I would need ot learn how to with non-standard residues and after reading through the manual endless times and searching on the web site and trying things I'm basically stuck. I thought it would easiest to deal with the triazole ring by creating it as a non-standard residue in aminoacids.n2t. As a starting point I thought I would try to work slowly by modifying an existing residue, so I arbitrary decided to modify alanine in order to understand how to work toward the more complicated triazole ring. So, in atomtypebyname.atp I copied the entry for ALA and called it ZZZ, and added a new entry ZZZ Protein into residuetypes.dat. At that point I can read in a pdb file with atoms belonging to residue ZZZ and pdb2gmx works fine. However, if I try to change one of the carbon atoms to a nitrogen, (say, chance CA to N or NA), I get errors (see below) that I'm having trouble interpreting. I thought that perhaps it was a problem of having two atoms with the same definition, so I made one N1 and one N2 as below, and also tried other variations (e.g., NA1 and NA2) Atom naming needs to be unique within the residue, so that grompp can later confirm that the order of the names in the topology and coordinate files match. (This is my entry in aminoacids.n2t) aminoacids.rtp I assume you mean. [ ZZZ ] [ atoms ] N1opls_238 -0.500 1 Hopls_2410.300 1 N2 opls_238 0.140 1 HAopls_1400.060 1 CBopls_135 -0.180 2 HB1opls_1400.060 2 HB2opls_1400.060 2 HB3opls_1400.060 2 Copls_2350.500 3 Oopls_236 -0.500 3 [ bonds ] N1 H N1N2 N2HA N2CB N2 C CB HB1 CB HB2 CB HB3 C O -C N1 [ impropers ] -CN2 N1 Himproper_Z_N_X_Y N2+N1 C Oimproper_O_C_X_Y I thought that this would lead to a structure that would connect C to the previous residue in my pdb file and the N to the next . However, when I do pdb2gmx, I get: *N2* to the next, but yeah... ** Back Off! I just backed up topol.top to ./#topol.top.40# Processing chain 1 (13 atoms, 1 residues) There are 0 donors and 1 acceptors There are 0 hydrogen bonds Identified residue ZZZ1 as a starting terminus. Identified residue ZZZ1 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Start terminus ZZZ-1: NH3+ End terminus ZZZ-1: COO- So the default(?) terminus selection is trying to give you charged termini (perhaps because the type is protein, but I'm not sure here). It is always appropriate to supply the command line you used. --- Program pdb2gmx, VERSION 4.5.3 Source code file: /build/buildd/gromacs-4.5.3/src/kernel/pdb2top.c, line: 1056 Fatal error: atom N not found in buiding block 1ZZZ while combining tdb and rtp aminoacids.n.tdb applies to protein residues and assumes that NH3+ can be applied. Evidently that won't work for your case. You will need to come up with some termini that make sense, or use more than one residue. I'm using the oplsaa force field, but up to this point it was a pretty arbitrary decision. I think my problem is understanding the mapping between atom names ( N1, HB1, etc) and the opls names, as I haven't yet found a good explanation for how this mapping is done and/or what flexibility one has in creating atom names for non-standard residues. (So, am I allowed to create a N atom and call it N1, as long as I assign it to an existing opls_xxx number ?) . Yes. Atom and residue names exist only for matching pieces of force fields together. The atom type determines the physics of the resulting model. The two are technically orthogonal, but in practice there are strong correlations. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Help with non-standard residues and molecular structures
Thanks-- that clarifies a lot. I hadn't quite realized how much is assumed about the residue terminii. It seems like I was trying to fit a square peg into a round hole. I'm going to re-think this and maybe take a different approach just based on using HETATMs and not trying to define a separate residue. The pdb file specification for HETATM still requires a residue name. I've found that using LIG seems to work. Any reason I shouldn't just continue using that, and define my molecule using HETATMs ? Thanks again for your help! Bob Hamers For something like what I'm trying to do, where Im using a pdb file that does not represent a protein, is On 1/4/2012 2:02 AM, Mark Abraham wrote: On 4/01/2012 4:57 PM, Robert Hamers wrote: I'd appreciate any help -- I'm trying to model a small (~ 20-carbon ) molecule linked to a diamond surface. I got the diamond surface with 1500 atoms working fine all the way through to the MD simulation and it looks great. But I'm getting stuck on the molecule, which is not a protein but a moderately short-chain molecule that has a triazole (N3C2) in the middle of it. I thought in order to make this work I would need ot learn how to with non-standard residues and after reading through the manual endless times and searching on the web site and trying things I'm basically stuck. I thought it would easiest to deal with the triazole ring by creating it as a non-standard residue in aminoacids.n2t. As a starting point I thought I would try to work slowly by modifying an existing residue, so I arbitrary decided to modify alanine in order to understand how to work toward the more complicated triazole ring. So, in atomtypebyname.atp I copied the entry for ALA and called it ZZZ, and added a new entry ZZZ Protein into residuetypes.dat. At that point I can read in a pdb file with atoms belonging to residue ZZZ and pdb2gmx works fine. However, if I try to change one of the carbon atoms to a nitrogen, (say, chance CA to N or NA), I get errors (see below) that I'm having trouble interpreting. I thought that perhaps it was a problem of having two atoms with the same definition, so I made one N1 and one N2 as below, and also tried other variations (e.g., NA1 and NA2) Atom naming needs to be unique within the residue, so that grompp can later confirm that the order of the names in the topology and coordinate files match. (This is my entry in aminoacids.n2t) aminoacids.rtp I assume you mean. [ ZZZ ] [ atoms ] N1opls_238 -0.500 1 Hopls_2410.300 1 N2 opls_238 0.140 1 HAopls_1400.060 1 CBopls_135 -0.180 2 HB1opls_1400.060 2 HB2opls_1400.060 2 HB3opls_1400.060 2 Copls_2350.500 3 Oopls_236 -0.500 3 [ bonds ] N1 H N1N2 N2HA N2CB N2 C CB HB1 CB HB2 CB HB3 C O -C N1 [ impropers ] -CN2 N1 Himproper_Z_N_X_Y N2+N1 C Oimproper_O_C_X_Y I thought that this would lead to a structure that would connect C to the previous residue in my pdb file and the N to the next . However, when I do pdb2gmx, I get: *N2* to the next, but yeah... ** Back Off! I just backed up topol.top to ./#topol.top.40# Processing chain 1 (13 atoms, 1 residues) There are 0 donors and 1 acceptors There are 0 hydrogen bonds Identified residue ZZZ1 as a starting terminus. Identified residue ZZZ1 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Start terminus ZZZ-1: NH3+ End terminus ZZZ-1: COO- So the default(?) terminus selection is trying to give you charged termini (perhaps because the type is protein, but I'm not sure here). It is always appropriate to supply the command line you used. --- Program pdb2gmx, VERSION 4.5.3 Source code file: /build/buildd/gromacs-4.5.3/src/kernel/pdb2top.c, line: 1056 Fatal error: atom N not found in buiding block 1ZZZ while combining tdb and rtp aminoacids.n.tdb applies to protein residues and assumes that NH3+ can be applied. Evidently that won't work for your case. You will need to come up with some termini that make sense, or use more than one residue. I'm using the oplsaa force field, but up to this point it was a pretty arbitrary decision. I think my problem is understanding the mapping between atom names ( N1, HB1, etc) and the opls names, as I haven't yet found a good explanation for how this mapping is done and/or what flexibility one has in creating atom names for non-standard residues. (So, am I allowed to create a N atom and call it N1, as long as I assign it to an existing opls_xxx number ?) . Yes. Atom and residue names exist only for matching pieces of force fields together. The atom type determines the physics of the resulting model. The two
[gmx-users] Help with non-standard residues and molecular structures
I'd appreciate any help -- I'm trying to model a small (~ 20-carbon ) molecule linked to a diamond surface. I got the diamond surface with 1500 atoms working fine all the way through to the MD simulation and it looks great. But I'm getting stuck on the molecule, which is not a protein but a moderately short-chain molecule that has a triazole (N3C2) in the middle of it. I thought in order to make this work I would need ot learn how to with non-standard residues and after reading through the manual endless times and searching on the web site and trying things I'm basically stuck. I thought it would easiest to deal with the triazole ring by creating it as a non-standard residue in aminoacids.n2t. As a starting point I thought I would try to work slowly by modifying an existing residue, so I arbitrary decided to modify alanine in order to understand how to work toward the more complicated triazole ring. So, in atomtypebyname.atp I copied the entry for ALA and called it ZZZ, and added a new entry ZZZ Protein into residuetypes.dat. At that point I can read in a pdb file with atoms belonging to residue ZZZ and pdb2gmx works fine. However, if I try to change one of the carbon atoms to a nitrogen, (say, chance CA to N or NA), I get errors (see below) that I'm having trouble interpreting. I thought that perhaps it was a problem of having two atoms with the same definition, so I made one N1 and one N2 as below, and also tried other variations (e.g., NA1 and NA2) (This is my entry in aminoacids.n2t) [ ZZZ ] [ atoms ] N1opls_238 -0.500 1 Hopls_2410.300 1 N2 opls_238 0.140 1 HAopls_1400.060 1 CBopls_135 -0.180 2 HB1opls_1400.060 2 HB2opls_1400.060 2 HB3opls_1400.060 2 Copls_2350.500 3 Oopls_236 -0.500 3 [ bonds ] N1 H N1N2 N2HA N2CB N2 C CB HB1 CB HB2 CB HB3 C O -C N1 [ impropers ] -CN2 N1 Himproper_Z_N_X_Y N2+N1 C Oimproper_O_C_X_Y I thought that this would lead to a structure that would connect C to the previous residue in my pdb file and the N to the next . However, when I do pdb2gmx, I get: ** Back Off! I just backed up topol.top to ./#topol.top.40# Processing chain 1 (13 atoms, 1 residues) There are 0 donors and 1 acceptors There are 0 hydrogen bonds Identified residue ZZZ1 as a starting terminus. Identified residue ZZZ1 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Start terminus ZZZ-1: NH3+ End terminus ZZZ-1: COO- --- Program pdb2gmx, VERSION 4.5.3 Source code file: /build/buildd/gromacs-4.5.3/src/kernel/pdb2top.c, line: 1056 Fatal error: atom N not found in buiding block 1ZZZ while combining tdb and rtp I'm using the oplsaa force field, but up to this point it was a pretty arbitrary decision. I think my problem is understanding the mapping between atom names ( N1, HB1, etc) and the opls names, as I haven't yet found a good explanation for how this mapping is done and/or what flexibility one has in creating atom names for non-standard residues. (So, am I allowed to create a N atom and call it N1, as long as I assign it to an existing opls_xxx number ?) . Any suggestions would be very welcome Thanks! Bob Hamers -- -- 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] Help with Principal component analysis
Dear all I run a MD on a GPCR (transmembrane protein) Then I run a PCA on results and I found 3PC sufficient to explain variance. On the same PC I get big values for samples located both at Nter (extracellular) and Cter (intracellular) or for similar cases such as both Nter(extracellular) and Loop5 (intracellular).According to you how could I explain the motion of group atoms intra and extracellular on the same components? Does it mean the motion of some atoms at Nter (for instance) could influence the motion at Cter ? Could it be logic?-- 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] Help with Principal component analysis
On 3/01/2012 6:54 AM, Alex Jemulin wrote: Dear all I run a MD on a GPCR (transmembrane protein) Then I run a PCA on results and I found 3PC sufficient to explain variance. On the same PC I get big values for samples located both at Nter (extracellular) and Cter (intracellular) or for similar cases such as both Nter(extracellular) and Loop5 (intracellular).According to you how could I explain the motion of group atoms intra and extracellular on the same components? Does it mean the motion of some atoms at Nter (for instance) could influence the motion at Cter ? Could it be logic? Highly unlikely. You don't give any details of your simulation, so your simulation could be too short, or have insufficient distance between your periodic images. 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] Help with g_density
Dear All I run g_density on a membrane protein. Here are the results http://elisacarli.altervista.org/densityhead.jpg http://elisacarli.altervista.org/tailsDensity.jpg Could you help me to give an interpretation to my analysis? Thank in advance-- 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] Help with g_density
What is your interpretation? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Alex Jemulin Sent: Tuesday, 20 December 2011 7:57 AM To: gmx-users@gromacs.org Subject: [gmx-users] Help with g_density Dear All I run g_density on a membrane protein. Here are the results http://elisacarli.altervista.org/densityhead.jpg http://elisacarli.altervista.org/tailsDensity.jpg Could you help me to give an interpretation to my analysis? Thank in advance -- 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] Help with g_rmsf
Hi everyone, please I have a litle problem: during my simulation, the dimer I'm simulating changed a lot. So when I calculate with g_rms, the RMSD between my initial and my final structure (choosing Protein-H), I get a value of 10 angstroms. However, when I try to calculate a RMSDeviation averaged over residue using g_rmsf -od , between the first chain of the initial and final structure, I get RMSDeviation per residue values that don't exceed 3 or 4 angstroms. Please can anyone explain how g_rmsf works? If I do the following: g_rmsf -s initial.pdb -f final.pdb -od rmsdev.xvg -res (I choose chainA-H), does g_rmsf fit one the whole dimer and then calculate rmsdeviation of chainA or does it fit on chainA and then calculate RMSdeviation of chainA. In the latter case, my result does not reflect the reality of my simulation. Please if anyone knows the answer, I would really appreciate some help. Thanks, Carla -- 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] Help with g_rmsf
Hi Carla, during my simulation, the dimer I'm simulating changed a lot. So when I calculate with g_rms, the RMSD between my initial and my final structure (choosing Protein-H), I get a value of 10 angstroms. Have you made sure there are no atoms jumping across the boundaries? g_rmsf -s initial.pdb -f final.pdb -od rmsdev.xvg -res (I choose chainA-H), If you choose chainA-H, you'll get results for that chain. It will be used for the fit as well as for the analysis. does g_rmsf fit one the whole dimer and then calculate rmsdeviation of chainA or does it fit on chainA and then calculate RMSdeviation of chainA. In the latter case, my result does not reflect the reality of my simulation. It does reflect the reality of your simulation. Maybe it does not reflect what you aimed to get. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] Help OPLS-AA system explodes
Dear Gromacs Users: I've been working with small unsaturated hydrocarbons using OPLS-AA with NVT calculations using box dimensions according to : x=y z=3x centered in 1/2x,1/2y,1/2z in order to obtain surface tension. My system expands at the begging of the mdrun calculation until it occupies the whole box uniformly. The mdp file i'm using its: ; VARIOUS PREPROCESSING OPTIONS title= Yo cpp = /usr/bin/cpp include = define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.003 nsteps = 40 ; For exact run continuation or redoing part of a run init_step= 0 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Temperature, friction coefficient (amu/ps) and random seed ;bd-temp = 300 ;bd-fric = 0 ;ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 100 emstep = 0.01 ; Max number of iterations in relax_shells niter= 20 ; Step size (1/ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1000 nstvout = 1000 nstfout = 1000 ; Checkpointing helps you continue after crashes nstcheckpoint= 1000 ; Output frequency for energies to log file and energy file nstlog = 50 nstenergy= 50 ; Output frequency and precision for xtc file nstxtcout= 50 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist= 1.4 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.4 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r= 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 1.4 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = berendsen ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t= 0.1 ref_t= 330 ; Pressure coupling Pcoupl = no Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ; Random seed for Andersen thermostat ondersen_seed= 815131 ; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic) annealing= no ; Number of time points to use for specifying annealing in each group annealing_npoints= ; List
Re: [gmx-users] help on mdrun
I am not sure I can give an affirmative working answer, but you may check ssh to each node, use top to see whether it's really run or just occupy the node but not use. On Sat, Jul 9, 2011 at 8:56 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 9/07/2011 3:37 AM, raghu...@bcpindia.org wrote: Hi I have a problem related to submitting a mdrun job on cluster. I tried to ask help or gromacs and rocks users-group. My machine specs. Cluster of Intel Xeon processors:QC with Rocks Cluster. 8 processors (16 threads) When I submit mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg on the localhost, the job takes note of 16 threads and the job completes in a day. But when I try submitting it to the cluster using following qsub script the job takes ~16 days --- #!/bin/bash # #$ -cwd #$ -S /bin/bash # #$ -N umbrella0 #$ -e umbrella0.errout #$ -o umbrella0.out # #$ -pe mpi 16 echo -n Running on: /opt/openmpi/bin/mpirun -np 16 -machinefile /home/raghuvir/machines /share/apps/gromacs-4.5.3/bin/mdrunmpi -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg echo Done. --- That's fine as far as GROMACS is concerned, so long as mdrunmpi really has been compiled with MPI. You can get what diagnostic information it knows about the MPI setup from the very top of the .log file. Otherwise, you'll have troubleshoot your use of MPI and your batch queue system. Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Best Regards, lina -- 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] help on mdrun
Hi I have a problem related to submitting a mdrun job on cluster. I tried to ask help or gromacs and rocks users-group. My machine specs. Cluster of Intel Xeon processors:QC with Rocks Cluster. 8 processors (16 threads) When I submit mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg on the localhost, the job takes note of 16 threads and the job completes in a day. But when I try submitting it to the cluster using following qsub script the job takes ~16 days --- #!/bin/bash # #$ -cwd #$ -S /bin/bash # #$ -N umbrella0 #$ -e umbrella0.errout #$ -o umbrella0.out # #$ -pe mpi 16 echo -n Running on: /opt/openmpi/bin/mpirun -np 16 -machinefile /home/raghuvir/machines /share/apps/gromacs-4.5.3/bin/mdrunmpi -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg echo Done. --- Please help me if possible Thanks N Regards Raghuvir -- 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] help on mdrun
On 9/07/2011 3:37 AM, raghu...@bcpindia.org wrote: Hi I have a problem related to submitting a mdrun job on cluster. I tried to ask help or gromacs and rocks users-group. My machine specs. Cluster of Intel Xeon processors:QC with Rocks Cluster. 8 processors (16 threads) When I submit mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg on the localhost, the job takes note of 16 threads and the job completes in a day. But when I try submitting it to the cluster using following qsub script the job takes ~16 days --- #!/bin/bash # #$ -cwd #$ -S /bin/bash # #$ -N umbrella0 #$ -e umbrella0.errout #$ -o umbrella0.out # #$ -pe mpi 16 echo -n Running on: /opt/openmpi/bin/mpirun -np 16 -machinefile /home/raghuvir/machines /share/apps/gromacs-4.5.3/bin/mdrunmpi -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg echo Done. --- That's fine as far as GROMACS is concerned, so long as mdrunmpi really has been compiled with MPI. You can get what diagnostic information it knows about the MPI setup from the very top of the .log file. Otherwise, you'll have troubleshoot your use of MPI and your batch queue system. 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] help
Hi, I'm doing implicit solvent in gromacs 4.5.2 with amber03 force field .I have done energy minimization .Then mdrun in NVT,but there is always LINCS error .When I make impolicit_solvent=no,it can run successfully. Is there a problem in the parameter settings? How can I solve the problem? Step 49, time 0.049 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 56.816425, max 1019.791504 (between atoms 2943 and 2942) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2913 2912 90.10.1093 62.1434 0.1093 2920 2919 91.30.1093 4.7180 0.1093 2943 2942 90.10.1895 99.4251 0.0974 Wrote pdb files with previous and current coordinates mdp file is in the attachment. md.mdp Description: Binary data -- 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] help
On 8/07/2011 1:31 PM, wrote: Hi, I'm doing implicit solvent in gromacs 4.5.2 with amber03 force field .I have done energy minimization .Then mdrun in NVT,but there is always LINCS error .When I make impolicit_solvent=no,it can run successfully. Is there a problem in the parameter settings? How can I solve the problem? Step 49, time 0.049 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 56.816425, max 1019.791504 (between atoms 2943 and 2942) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2913 2912 90.1 0.1093 62.1434 0.1093 2920 2919 91.3 0.1093 4.7180 0.1093 2943 2942 90.1 0.1895 99.4251 0.0974 Wrote pdb files with previous and current coordinates mdp file is in the attachment. There's a few threads like this in the archives. Probably a smaller time step while equilibrating is in order. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Help: Gromacs Installation
Dear Mark Abraham all, We used another benchmarking systems, such as d.dppc on 4 processors, but we have the same problem (1 proc use about 100%, the others 0%). After for a while we receive the following error: Working directory is /localuser/armen/d.dppc Running on host wn1.ysu-cluster.grid.am Time is Fri Apr 22 13:55:47 AMST 2011 Directory is /localuser/armen/d.dppc START Start: Fri Apr 22 13:55:47 AMST 2011 p2_487: p4_error: Timeout in establishing connection to remote process: 0 rm_l_2_500: (301.160156) net_send: could not write to fd=5, errno = 32 p2_487: (301.160156) net_send: could not write to fd=5, errno = 32 p0_32738: p4_error: net_recv read: probable EOF on socket: 1 p3_490: (301.160156) net_send: could not write to fd=6, errno = 104 p3_490: p4_error: net_send write: -1 p3_490: (305.167969) net_send: could not write to fd=5, errno = 32 p0_32738: (305.371094) net_send: could not write to fd=4, errno = 32 p1_483: p4_error: net_recv read: probable EOF on socket: 1 rm_l_1_499: (305.167969) net_send: could not write to fd=5, errno = 32 p1_483: (311.171875) net_send: could not write to fd=5, errno = 32 Fri Apr 22 14:00:59 AMST 2011 End: Fri Apr 22 14:00:59 AMST 2011 END We tried new version of Gromacs, but receive the same error. Please, help us to overcome the problem. With regards, Hrach On 4/22/11 1:41 PM, Mark Abraham wrote: On 4/22/2011 5:40 PM, Hrachya Astsatryan wrote: Dear all, I would like to inform you that I have installed the gromacs4.0.7 package on the cluster (nodes of the cluster are 8 core Intel, OS: RHEL4 Scientific Linux) with the following steps: yum install fftw3 fftw3-devel ./configure --prefix=/localuser/armen/gromacs --enable-mpi Also I have downloaded gmxbench-3.0 package and try to run d.villin to test it. Unfortunately it wok fine until np is 1,2,3, if I use more than 3 procs I receive low CPU balancing and the process in hanging. Could you, please, help me to overcome the problem? Probably you have only four physical cores (hyperthreading is not normally useful), or your MPI is configured to use only four cores, or these benchmarks are too small to scale usefully. Choosing to do a new installation of a GROMACS version that is several years old is normally less productive than the latest version. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Help: Gromacs Installation
This seems to be a problem with your MPI library. Test to see whether other MPI programs don't have the same problem. If it is not GROMACS specific please ask on the mailinglist of your MPI library. If it only happens with GROMACS be more specific about what your setup is (what MPI library, what hardware, ...). Also you could use the latest GROMACS 4.5.x. It has built in thread support and doesn't need MPI as long as you only run on n cores within one SMP node. Roland On Wed, Apr 27, 2011 at 2:13 PM, Hrachya Astsatryan hr...@sci.am wrote: Dear Mark Abraham all, We used another benchmarking systems, such as d.dppc on 4 processors, but we have the same problem (1 proc use about 100%, the others 0%). After for a while we receive the following error: Working directory is /localuser/armen/d.dppc Running on host wn1.ysu-cluster.grid.am Time is Fri Apr 22 13:55:47 AMST 2011 Directory is /localuser/armen/d.dppc START Start: Fri Apr 22 13:55:47 AMST 2011 p2_487: p4_error: Timeout in establishing connection to remote process: 0 rm_l_2_500: (301.160156) net_send: could not write to fd=5, errno = 32 p2_487: (301.160156) net_send: could not write to fd=5, errno = 32 p0_32738: p4_error: net_recv read: probable EOF on socket: 1 p3_490: (301.160156) net_send: could not write to fd=6, errno = 104 p3_490: p4_error: net_send write: -1 p3_490: (305.167969) net_send: could not write to fd=5, errno = 32 p0_32738: (305.371094) net_send: could not write to fd=4, errno = 32 p1_483: p4_error: net_recv read: probable EOF on socket: 1 rm_l_1_499: (305.167969) net_send: could not write to fd=5, errno = 32 p1_483: (311.171875) net_send: could not write to fd=5, errno = 32 Fri Apr 22 14:00:59 AMST 2011 End: Fri Apr 22 14:00:59 AMST 2011 END We tried new version of Gromacs, but receive the same error. Please, help us to overcome the problem. With regards, Hrach On 4/22/11 1:41 PM, Mark Abraham wrote: On 4/22/2011 5:40 PM, Hrachya Astsatryan wrote: Dear all, I would like to inform you that I have installed the gromacs4.0.7 package on the cluster (nodes of the cluster are 8 core Intel, OS: RHEL4 Scientific Linux) with the following steps: yum install fftw3 fftw3-devel ./configure --prefix=/localuser/armen/gromacs --enable-mpi Also I have downloaded gmxbench-3.0 package and try to run d.villin to test it. Unfortunately it wok fine until np is 1,2,3, if I use more than 3 procs I receive low CPU balancing and the process in hanging. Could you, please, help me to overcome the problem? Probably you have only four physical cores (hyperthreading is not normally useful), or your MPI is configured to use only four cores, or these benchmarks are too small to scale usefully. Choosing to do a new installation of a GROMACS version that is several years old is normally less productive than the latest version. 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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Help: Gromacs Installation
Dear Roland, We need to run the GROMACS on the base of the nodes of our cluster (in order to use all computational resources of the cluster), that's why we need MPI (instead of using thread or OpenMP within the SMP node). I can run simple MPI examples, so I guess the problem on the implementation of the Gromacs. Regads, Hrach On 4/27/11 11:29 PM, Roland Schulz wrote: This seems to be a problem with your MPI library. Test to see whether other MPI programs don't have the same problem. If it is not GROMACS specific please ask on the mailinglist of your MPI library. If it only happens with GROMACS be more specific about what your setup is (what MPI library, what hardware, ...). Also you could use the latest GROMACS 4.5.x. It has built in thread support and doesn't need MPI as long as you only run on n cores within one SMP node. Roland On Wed, Apr 27, 2011 at 2:13 PM, Hrachya Astsatryan hr...@sci.am mailto:hr...@sci.am wrote: Dear Mark Abraham all, We used another benchmarking systems, such as d.dppc on 4 processors, but we have the same problem (1 proc use about 100%, the others 0%). After for a while we receive the following error: Working directory is /localuser/armen/d.dppc Running on host wn1.ysu-cluster.grid.am http://wn1.ysu-cluster.grid.am Time is Fri Apr 22 13:55:47 AMST 2011 Directory is /localuser/armen/d.dppc START Start: Fri Apr 22 13:55:47 AMST 2011 p2_487: p4_error: Timeout in establishing connection to remote process: 0 rm_l_2_500: (301.160156) net_send: could not write to fd=5, errno = 32 p2_487: (301.160156) net_send: could not write to fd=5, errno = 32 p0_32738: p4_error: net_recv read: probable EOF on socket: 1 p3_490: (301.160156) net_send: could not write to fd=6, errno = 104 p3_490: p4_error: net_send write: -1 p3_490: (305.167969) net_send: could not write to fd=5, errno = 32 p0_32738: (305.371094) net_send: could not write to fd=4, errno = 32 p1_483: p4_error: net_recv read: probable EOF on socket: 1 rm_l_1_499: (305.167969) net_send: could not write to fd=5, errno = 32 p1_483: (311.171875) net_send: could not write to fd=5, errno = 32 Fri Apr 22 14:00:59 AMST 2011 End: Fri Apr 22 14:00:59 AMST 2011 END We tried new version of Gromacs, but receive the same error. Please, help us to overcome the problem. With regards, Hrach On 4/22/11 1:41 PM, Mark Abraham wrote: On 4/22/2011 5:40 PM, Hrachya Astsatryan wrote: Dear all, I would like to inform you that I have installed the gromacs4.0.7 package on the cluster (nodes of the cluster are 8 core Intel, OS: RHEL4 Scientific Linux) with the following steps: yum install fftw3 fftw3-devel ./configure --prefix=/localuser/armen/gromacs --enable-mpi Also I have downloaded gmxbench-3.0 package and try to run d.villin to test it. Unfortunately it wok fine until np is 1,2,3, if I use more than 3 procs I receive low CPU balancing and the process in hanging. Could you, please, help me to overcome the problem? Probably you have only four physical cores (hyperthreading is not normally useful), or your MPI is configured to use only four cores, or these benchmarks are too small to scale usefully. Choosing to do a new installation of a GROMACS version that is several years old is normally less productive than the latest version. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov http://cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
