[Fwd: Re: [gmx-users] VSMP cluster performance changes with time]
I am using 24 processors and it is same for all steps. this is the command in use: tpbconv_mpi -f run.trr -s run.tpr -e run.edr -extend 1000 -o ext_11 nohup /opt/ScaleMP/mpich2/1.0.8/bin/mpirun -machinefile $PBS_NODEFILE -np 24 /opt/gromacs4/bin/mdrun_mpi -v -deffnm ext_11 -- similar for next steps. regards anupam On 18/08/11, Anupam Nath Jha anu...@mbu.iisc.ernet.in wrote: Dear all I am running a MD (Gromacs - 4.5.3) in VSMP cluster with 24nodes. I am writing log files for different ns (1-10) in different files i.e. different files for each nano second . The performance goes like following: -- for 1st ns: (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 1444.719 85.902 3.946 6.082 Finished mdrun on node 0 Tue Aug 16 21:46:02 2011 at 2nd ns: (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance:560.393 33.322 1.531 15.679 Finished mdrun on node 0 Wed Aug 17 13:27:38 2011 -- and in case of 3rd ns: it didn't complete the all steps and went in next. Is it the problem with the gromacs? Probably not. Assuming you have kept everything else constant, it is likely that other activity on the machine or file system is delaying you somehow. However, in the absence of much basic information (like how many processors you are trying to use) we can't suppose much. Copying and pasting command lines is useful. Mark -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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 -- Science is facts; just as houses are made of stone, so is science is made of facts; but a pile of stones is not a house, and a collection of facts is not necessarily science. Anupam Nath Jha Saraswathi Vishveshwara Lab Molecular Biophysics Unit IISc,Bangalore-560012 Karnataka Ph. no.-22932611 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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 -- Science is facts; just as houses are made of stone, so is science is made of facts; but a pile of stones is not a house, and a collection of facts is not necessarily science. Anupam Nath Jha Saraswathi Vishveshwara Lab Molecular Biophysics Unit IISc,Bangalore-560012 Karnataka Ph. no.-22932611 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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: [Fwd: Re: [gmx-users] VSMP cluster performance changes with time]
On 19/08/2011 5:07 PM, Anupam Nath Jha wrote: Is it the problem with the gromacs? Probably not. Assuming you have kept everything else constant, it is likely that other activity on the machine or file system is delaying you somehow. This is still likely to be true. Other activity (other users jobs, heavy I/O demand etc.) can starve GROMACS for resources. If you are doing everything the same, then something you are not controlling must be different. 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] calculate residence time for a protein complex
Hi, I have simulated a protein complex and now i would like to know the residing water molecules between the protein complex. g_hbond and trjorder helps in giving the number of hydrogen bonds and distance. but is this the residence time calculation. please help me with this. there few posts given in the archives regarding the residence time which is not very clear to me. but will the residence time calculation same for single protein and complex Thank you, Aiswarya -- 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] Regarding generating topology file.
On Tuesday, August 2, 2011 at 5:17 AM, Ravi Kumar Venkatraman ravi.ipc.i...@gmail.com wrote: I have got some topology and parameter file for some small organic molecules from swissparam in *.mol2 format. I am trying to generate *.top, *.gro *.itp files using topolbuild. But I dont know how to do. So can anybody give me a link or some materials related to this. I'm not sure what the problem is. The topolbuild 1.3.1 download does include documentation on how to use it. Is there something specific you have tried that you are having difficulties with? Of course, for use with gromacs 4.5.*, one does have edit the *.top with a text editor to change the initial include lines in the topology file to reflect the re-organization of the force field files. Furthermore, the current topolbuild version does not support CHARMm force fields. Also, I believe that swissparam gives those files. -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273-- 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] -ter option with pdb2gmx
Hello, I am trying to use -ter with the pdb2gmx command, seems its not working fine. pdb2gmx -f file.pdb -o file.gro. -p file.top -ter I also used -inter option, its not working. I am using 4.5.4 version. any help would be greatly appreciated. Regards, vijay -- 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] more than 100% CPU
Thank you so much, all. Jae H. Park -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Szilárd Páll Sent: Thursday, August 18, 2011 9:19 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] more than 100% CPU It is true that on Intel CPUs with HT supported and on you get an up to 10-15% speedup if you also use all virtual cores wrt to running only as many threads as real cores. Additionally, as the OS reports all virtual processors, by Gromacs will use all of them by default, i.e. will run with 8 threads on a 4-core CPU with HT. However, this is not the case on AMD and other CPU without simultaneous multithreading. There you'll loose performance if you overload CPUs. -- Szilárd On Fri, Aug 19, 2011 at 3:52 AM, chris.ne...@utoronto.ca wrote: Slightly off-topic, but for all but the smallest systems, I get a further 10% efficiency by running a 16-process mpi job on an 8-core machine. I suspect that the story is the same with threads. Thus, on a 16-core node, you could try starting 32 threads. Note that this will report a 2x larger efficiency as you were discussing before, but by checking the ns.day you will see that the benefit is between 5% and 16% Chris. It means you are running a lot of parallel processes, but that does not translate into a linear increase in speed. So faster, but not 16X. Warren Gallin On 2011-08-18, at 5:36 PM, Park, Jae Hyun nmn wrote: Thank you, Warren. Does that mean 16 times faster ? Jae H. Park -Original Message- From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Warren Gallin Sent: Thursday, August 18, 2011 7:26 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] more than 100% CPU I believe that the current version of GROMACS supports threading, which does not require mpi. So mdrun is running threads at 100% of the activity of each of your 16 nodes, hence 1600%. Warren Gallin On 2011-08-18, at 5:19 PM, Park, Jae Hyun nmn wrote: Hi GMX users, I installed GMX 4.5.3 recently. But, when I just execute mdrun (without mpi, I did not installed mpi-version of mdrun), the use of CPU appears more than 100% (top command in LINUX). How is it possible? For example, I am using 16-node machine. And if I simply run mdrun, then use of CPU is 1600%!!. The simulation runs well and the results looks reasonable. Is there anybody who can teach me what is happening? I would deeply appreciate. -- gmx-users mailing list gmx-users@gromacs.org hxxp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at hxxp://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read hxxp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org hxxp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at hxxp://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 hxxp://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] use of the mailing list
Sure Mark. If your interest is in patrolling the Gromacs mailing list, then I'll leave you to it. On Thu, Aug 18, 2011 at 9:40 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 19/08/2011 1:41 PM, Junior Nebeker wrote: Correct. Other people (who are new to this list) need your help, and unless their requests are way out of line, there's no reason to adopt a haughty attitude in responding. There's never a case for rudeness, but when (for example) people have been asking questions on the mailing list for years and still haven't absorbed the advice available here http://www.gromacs.org/Support, then one can get frustrated. Expressing a little of that can help people realise how to participate more effectively in the discussion. One's family doctor can ask a lot of patient questions about what is wrong because you're paying them a lot of money. If people who might give free help don't feel that their time is valued, they might stop giving it. One way of demonstrating this is to ask questions that show one's willingness to work on the problem by providing lots of relevant diagnostic information. See http://www.catb.org/~esr/faqs/smart-questions.html Mark P.S. I'm not intending to express particular criticism of the original poster in this thread On Thu, Aug 18, 2011 at 5:05 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 19/08/2011 9:32 AM, Junior Nebeker wrote: Hey mark, If you are really sick of asking people for such information, why do you even care to respond to this mailing list? Because I'd rather teach someone to fish than either give them fish or watch them starve. 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 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] use of the mailing list
On 20/08/2011 1:13 AM, Junior Nebeker wrote: Sure Mark. If your interest is in patrolling the Gromacs mailing list, then I'll leave you to it. If you have something constructive to contribute, please do. Otherwise, please don't. 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] Possible bug in g_hbond with implicit solvent
Hi All, I wanted to solicit some feedback on what I think may be a bug related to periodicity handling and/or implicit solvent simulations. I ran some simulations of a few model peptides (some helices, hairpins, etc) and I got what I believed to be very inflated results for backbone hydrogen bonds. For instance, a helical peptide with only 17 residues had, on average, 23.5 hydrogen bonds within the backbone alone, which, judging from the configurations, couldn't really be possible. The simulations use infinite cutoffs and a nonperiodic unit cell. g_hbond identifies 26 backbone hydrogen bonds at time zero of the trajectory. If, however, I create a .tpr file from a configuration with a large box (i.e., 10-nm cube) and run g_hbond on just that configuration (.gro file), I get a far more sensible result - 8 hydrogen bonds. I can't recall anyone reporting anything like this before, but it seems to be that it's a fairly important issue. Before I posted to redmine, I wanted to see if anyone had encountered this, too. The version I'm using is 4.5.4; I haven't tested the latest release-4-5-patches yet, but I can if that would be useful. -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] -ter option with pdb2gmx
-ter or -inter options of pdb2gmx are working fine with all force fields except amber force field. I cant select the terminal groups when I use amber ff, it directly goes through the generation of top files without asking any options for terminal group selection. I just want to use the none option for the terminals (with amber ff). any suggestion? Regards, Vijay Date: Fri, 19 Aug 2011 15:31:04 +0200 From: Vijayaraj vijayara...@gmail.com Subject: [gmx-users] -ter option with pdb2gmx To: gmx-users@gromacs.org Message-ID: CAE-dxS-xCLP=pVjgERGKm2yoj0qO=2B7QQQx5p=5Wa=vaj4...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hello, I am trying to use -ter with the pdb2gmx command, seems its not working fine. pdb2gmx -f file.pdb -o file.gro -p file.top -ter I also used -inter option, its not working. I am using 4.5.4 version. any help would be greatly appreciated. Regards, vijay -- 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] Possible bug in g_hbond with implicit solvent
On 20/08/2011 1:26 AM, Justin A. Lemkul wrote: Hi All, I wanted to solicit some feedback on what I think may be a bug related to periodicity handling and/or implicit solvent simulations. I ran some simulations of a few model peptides (some helices, hairpins, etc) and I got what I believed to be very inflated results for backbone hydrogen bonds. For instance, a helical peptide with only 17 residues had, on average, 23.5 hydrogen bonds within the backbone alone, which, judging from the configurations, couldn't really be possible. Does the structure file input to g_hbond have a spuriously small box? Mark The simulations use infinite cutoffs and a nonperiodic unit cell. g_hbond identifies 26 backbone hydrogen bonds at time zero of the trajectory. If, however, I create a .tpr file from a configuration with a large box (i.e., 10-nm cube) and run g_hbond on just that configuration (.gro file), I get a far more sensible result - 8 hydrogen bonds. I can't recall anyone reporting anything like this before, but it seems to be that it's a fairly important issue. Before I posted to redmine, I wanted to see if anyone had encountered this, too. The version I'm using is 4.5.4; I haven't tested the latest release-4-5-patches yet, but I can if that would be useful. -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] -ter option with pdb2gmx
On 20/08/2011 1:27 AM, Vijayaraj wrote: -ter or -inter options of pdb2gmx are working fine with all force fields except amber force field. I cant select the terminal groups when I use amber ff, it directly goes through the generation of top files without asking any options for terminal group selection. I just want to use the none option for the terminals (with amber ff). any suggestion? AMBER treats charges on terminal residues differently, so the -ter mechanism doesn't work in the way that it can for other force fields. See http://ffamber.cnsm.csulb.edu/#usage. You'd have found this out faster if your earlier email had had a one-sentence description of your simulation objective. :) Mark Regards, Vijay Date: Fri, 19 Aug 2011 15:31:04 +0200 From: Vijayaraj vijayara...@gmail.com mailto:vijayara...@gmail.com Subject: [gmx-users] -ter option with pdb2gmx To: gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: CAE-dxS-xCLP=pVjgERGKm2yoj0qO=2B7QQQx5p=5Wa=vaj4...@mail.gmail.com mailto:vaj4...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hello, I am trying to use -ter with the pdb2gmx command, seems its not working fine. pdb2gmx -f file.pdb -o file.gro -p file.top -ter I also used -inter option, its not working. I am using 4.5.4 version. any help would be greatly appreciated. Regards, vijay -- 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] Possible bug in g_hbond with implicit solvent
Mark Abraham wrote: On 20/08/2011 1:26 AM, Justin A. Lemkul wrote: Hi All, I wanted to solicit some feedback on what I think may be a bug related to periodicity handling and/or implicit solvent simulations. I ran some simulations of a few model peptides (some helices, hairpins, etc) and I got what I believed to be very inflated results for backbone hydrogen bonds. For instance, a helical peptide with only 17 residues had, on average, 23.5 hydrogen bonds within the backbone alone, which, judging from the configurations, couldn't really be possible. Does the structure file input to g_hbond have a spuriously small box? It does, and I suspect this is where the problem ultimately lies. For the simulation, with pbc = no the box vectors get ignored and everything is fine. For analysis, however, it seems that the PBC routines are still trying to fit everything into that tiny box and thus basically all possible H-bonds are detected as being present because the distances are so small. Re-generating the .tpr file with a new, larger, box does not fix the problem, likely because the .xtc still has the tiny box. Manipulating the trajectory with trjconv -box -center seems to work, though. So I suppose this is an acceptable workaround, though it still may be a problem worth looking into. Thanks for the inspiration; hadn't thought about trying to change the box after the fact :) -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] g_rdf
Hello, I run a 5ns simulation for a single glucose molecule in gas phase. I tried to plot radial distribution function for O---H intramolecular interactions using following command. g_rdf -f 6.trr -s 6.tpr -n index -o In rdf.xvg file there is no data. Can you tell what could be the reason. I am using Gromacs 4.0.7 version. Thanks Nilesh -- 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] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure
I have sent this email days ago, but I got no answer. Hope someone would saw it this time. Sorry for disturbing. Dear all: I am using gromacs-4.0.2_localpressure to calculate the local pressure of my system. I have a question. When rerun the mdrun from gromacs-4.0.2_localpressure I used a new .mdp file. There are some changes of the new .mdp file according the original one. I have 2 questions: 1. I changed the The coulomb interaction type from PME to reaction field with epsilon_r=1 epsilon_rf=78; Is this change feasible? 2. I used LINCS for all bonds in the simulation, and I still use the LINCS for all bonds when calculate the local pressure. Is this way right? Thanks for any reply. Best wishes, KONG Xian Tsinghua, Beijing, China -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_rdf
Nilesh Dhumal wrote: Hello, I run a 5ns simulation for a single glucose molecule in gas phase. I tried to plot radial distribution function for O---H intramolecular interactions using following command. g_rdf -f 6.trr -s 6.tpr -n index -o In rdf.xvg file there is no data. Can you tell what could be the reason. Probably due to exclusions in the topology, as g_rdf -h indicates. There are several possible workarounds discussed in the same paragraph. -Justin I am using Gromacs 4.0.7 version. Thanks Nilesh -- 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] Possible bug in g_hbond with implicit solvent
On 20/08/2011 1:45 AM, Justin A. Lemkul wrote: Mark Abraham wrote: On 20/08/2011 1:26 AM, Justin A. Lemkul wrote: Hi All, I wanted to solicit some feedback on what I think may be a bug related to periodicity handling and/or implicit solvent simulations. I ran some simulations of a few model peptides (some helices, hairpins, etc) and I got what I believed to be very inflated results for backbone hydrogen bonds. For instance, a helical peptide with only 17 residues had, on average, 23.5 hydrogen bonds within the backbone alone, which, judging from the configurations, couldn't really be possible. Does the structure file input to g_hbond have a spuriously small box? It does, and I suspect this is where the problem ultimately lies. For the simulation, with pbc = no the box vectors get ignored and everything is fine. For analysis, however, it seems that the PBC routines are still trying to fit everything into that tiny box and thus basically all possible H-bonds are detected as being present because the distances are so small. Sure. In your case, mdrun learns to ignore the box from the .mdp file setting, but I presume the box values still get copied around in the same fashion as for NVT PBC... A pre-emptive work-around might be to generate the simulation .tpr with a spurious large box, which then gets transferred everywhere else. Better file formats would be the only reasonable fix, and that would not be all that reasonable... I don't know how to avoid people rediscovering this phenomenon in the future. Mark Re-generating the .tpr file with a new, larger, box does not fix the problem, likely because the .xtc still has the tiny box. Manipulating the trajectory with trjconv -box -center seems to work, though. So I suppose this is an acceptable workaround, though it still may be a problem worth looking into. Thanks for the inspiration; hadn't thought about trying to change the box after the fact :) -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] parameters for CH1 -- S -- CH2 ?
Hi all, I have a small molecule with a part like: CH1 --- CH1 --- S --- CH2 --- CH1 | CH1 I first tried PRODRG, and it turned out PRODRG assigned bond, angle, and dihedral parameters according what are already present in the gromos53a6.ff/ffbonded.itp file. Since this file does not contain information regarding this CH1 --- S --- CH2 pattern, PRODRG just assigned bond (gb_31),angle (ga_4) as if my molecule has CH3 --- S --- CH2 pattern, and dihedral parameters for CH1 -- CH1 -- S -- CH2 as if it was CH1 -- CH2 -- S -- CH2. So I guess I have to do this manually. But as no corresponding parameters defined in ffbonded.itp file, should I derive these parameters via chemical intuition and try validate them in some way? Or is there an easier alternative way to do this? Thanks for any suggestion! Yun -- 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] parameters for CH1 -- S -- CH2 ?
On 20/08/2011 1:57 AM, Yun Shi wrote: Hi all, I have a small molecule with a part like: CH1 --- CH1 --- S --- CH2 --- CH1 | CH1 I first tried PRODRG, and it turned out PRODRG assigned bond, angle, and dihedral parameters according what are already present in the gromos53a6.ff/ffbonded.itp file. Since this file does not contain information regarding this CH1 --- S --- CH2 pattern, PRODRG just assigned bond (gb_31),angle (ga_4) as if my molecule has CH3 --- S --- CH2 pattern, and dihedral parameters for CH1 -- CH1 -- S -- CH2 as if it was CH1 -- CH2 -- S -- CH2. So I guess I have to do this manually. But as no corresponding parameters defined in ffbonded.itp file, should I derive these parameters via chemical intuition and try validate them in some way? Or is there an easier alternative way to do this? Parameterizing new species is not easy. See http://www.gromacs.org/Documentation/How-tos/Parameterization. Be sure to check the literature for existing approaches - and particularly how the thioether parameters that do exist were derived. 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] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure
On Fri, Aug 19, 2011 at 8:50 AM, KONG Xian xiansh...@gmail.com wrote: I have sent this email days ago, but I got no answer. Hope someone would saw it this time. Sorry for disturbing. Dear all: I am using gromacs-4.0.2_localpressure to calculate the local pressure of my system. I have a question. When rerun the mdrun from gromacs-4.0.2_localpressure I used a new .mdp file. There are some changes of the new .mdp file according the original one. I have 2 questions: **1. **I changed the The coulomb interaction type from PME to reaction field with epsilon_r=1 epsilon_rf=78; Is this change feasible? Yes, you have to switch to cutoff for coulomb interaction. I have seen in other publications that they use a regular coulomb with cutoff as large as 2 nm. I am not sure whether there is any advantage in using Reaction field. **2. **I used LINCS for all bonds in the simulation, and I still use the LINCS for all bonds when calculate the local pressure. Is this way right? I have had no problems in using LINCS during local pressure calculation. ** ** Thanks for any reply. ** ** Best wishes, KONG Xian Tsinghua, Beijing, China __ Information from ESET NOD32 Antivirus, version of virus signature database 6393 (20110819) __ The message was checked by ESET NOD32 Antivirus. http://www.eset.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] use of the mailing list
On Fri, Aug 19, 2011 at 8:13 AM, Junior Nebeker junior.nebe...@gmail.comwrote: Sure Mark. If your interest is in patrolling the Gromacs mailing list, then I'll leave you to it. I think before you type your response you should consider that Mark has helped several hundred times over this mailing list. On Thu, Aug 18, 2011 at 9:40 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 19/08/2011 1:41 PM, Junior Nebeker wrote: Correct. Other people (who are new to this list) need your help, and unless their requests are way out of line, there's no reason to adopt a haughty attitude in responding. There's never a case for rudeness, but when (for example) people have been asking questions on the mailing list for years and still haven't absorbed the advice available here http://www.gromacs.org/Support, then one can get frustrated. Expressing a little of that can help people realise how to participate more effectively in the discussion. One's family doctor can ask a lot of patient questions about what is wrong because you're paying them a lot of money. If people who might give free help don't feel that their time is valued, they might stop giving it. One way of demonstrating this is to ask questions that show one's willingness to work on the problem by providing lots of relevant diagnostic information. See http://www.catb.org/~esr/faqs/smart-questions.html Mark P.S. I'm not intending to express particular criticism of the original poster in this thread On Thu, Aug 18, 2011 at 5:05 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 19/08/2011 9:32 AM, Junior Nebeker wrote: Hey mark, If you are really sick of asking people for such information, why do you even care to respond to this mailing list? Because I'd rather teach someone to fish than either give them fish or watch them starve. 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] h-bonds constraints
What criterion does the grompp utility use to identify H-atoms when it is requested in the MDP file to apply constraints=h-bonds? Thanks. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] h-bonds constraints
On Fri, Aug 19, 2011 at 20:02, Dr. Vitaly V. Chaban vvcha...@gmail.com wrote: What criterion does the grompp utility use to identify H-atoms when it is requested in the MDP file to apply constraints=h-bonds? Thanks. Any atom name starting with H or h (so case-insensitive). Cheers, Bogdan -- 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] h-bonds constraints
Thanks! That's reasonable. On Fri, Aug 19, 2011 at 2:31 PM, Bogdan Costescu bcoste...@gmail.com wrote: On Fri, Aug 19, 2011 at 20:02, Dr. Vitaly V. Chaban vvcha...@gmail.com wrote: What criterion does the grompp utility use to identify H-atoms when it is requested in the MDP file to apply constraints=h-bonds? Thanks. Any atom name starting with H or h (so case-insensitive). Cheers, Bogdan -- 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] use of the mailing list
Of course I know of Mark's contributions. However, one's contributions, big or small, shouldn't excuse him/her from being rude to others. That's my constructive feedback - take it or leave it. On Fri, Aug 19, 2011 at 9:51 AM, Amit Choubey kgp.a...@gmail.com wrote: On Fri, Aug 19, 2011 at 8:13 AM, Junior Nebeker junior.nebe...@gmail.comwrote: Sure Mark. If your interest is in patrolling the Gromacs mailing list, then I'll leave you to it. I think before you type your response you should consider that Mark has helped several hundred times over this mailing list. On Thu, Aug 18, 2011 at 9:40 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 19/08/2011 1:41 PM, Junior Nebeker wrote: Correct. Other people (who are new to this list) need your help, and unless their requests are way out of line, there's no reason to adopt a haughty attitude in responding. There's never a case for rudeness, but when (for example) people have been asking questions on the mailing list for years and still haven't absorbed the advice available here http://www.gromacs.org/Support, then one can get frustrated. Expressing a little of that can help people realise how to participate more effectively in the discussion. One's family doctor can ask a lot of patient questions about what is wrong because you're paying them a lot of money. If people who might give free help don't feel that their time is valued, they might stop giving it. One way of demonstrating this is to ask questions that show one's willingness to work on the problem by providing lots of relevant diagnostic information. See http://www.catb.org/~esr/faqs/smart-questions.html Mark P.S. I'm not intending to express particular criticism of the original poster in this thread On Thu, Aug 18, 2011 at 5:05 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 19/08/2011 9:32 AM, Junior Nebeker wrote: Hey mark, If you are really sick of asking people for such information, why do you even care to respond to this mailing list? Because I'd rather teach someone to fish than either give them fish or watch them starve. 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] NPT - density off
Dear experts, I am intending to calculate the equilibrium density of a pure hydrocarbon at different pressures , at 425 K. The normal boiling point of the liquid is around 350 K. For pressures below 100 bar densities I am getting from NPT is in accurate. I start form a structure which is compressed to above 0.6 g/cm3 density but since temperature is high density goes than to the values below. P = 50 bar NPT rho= 0.344 experimental density ~ 0.54 P100 NPT rho= 0.43 experimental density ~ 0.55 densities become more accurate for P 100 bar. P 500 rho= 0.56experimental density ~ 0.61 I thought maybe you have some idea on how this inaccuracy can be improved. Thank you in advance for your invaluable help. Best, ;Bonds constraints = none constraint-algorithm = lincs ;Run control integrator = md dt = 0.001 nsteps = 500 nstcomm = 100 ;Output control nstenergy = 100 nstxout = 100 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 1000 ;Neighbor searching nstlist = 10 ns_type = grid ;Electrostatics/VdW coulombtype = Shift vdw-type= Shift rcoulomb-switch = 0 rvdw-switch = 0.9 ;Cut-offs rlist = 1.25 rcoulomb= 1.0 rvdw= 1.0 ;Temperature coupling Tcoupl = v-rescale tc-grps = System tau_t = 0.1 ref_t = 425 ;Pressure coupling Pcoupl = berendsen Pcoupltype = isotropic tau_p = 1 compressibility = 3.5e-5 ref_p = 100 ;Velocity generation gen_vel = no;yes gen_temp= 425 gen_seed= 173529 -- 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] NPT - density off
Dear Email Sender, Thank you very much for contacting me! Unfortunately, I am not available in the office at the moment and cannot respond to your email. I will be able to handle your request starting again Monday, August 22, 2011. For all questions about CloudBroker and the CloudBroker Platform, please contact the company under i...@cloudbroker.com or Nicola Fantini under nicola.fant...@cloudbroker.com. If you need to talk to me in person for urgent or important issues, please call my mobile phone number. Kind regards, Wibke Sudholt -- Dr. Wibke Sudholt CEO CloudBroker GmbH Technoparkstrasse 1 CH-8005 Zurich Switzerland Phone: +41 44 633 79 34 Email: wibke.sudh...@cloudbroker.com Web:http://www.cloudbroker.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] GROMACS with GPU
Hi! If I may ask, but what is the gromacs version that is planned on the roadmap to begin to work with the newer version of openmm? Specially interested due to ATI support Regards Jones On Thu, Aug 18, 2011 at 10:01 PM, Szilárd Páll szilard.p...@cbr.su.sewrote: Hi, Gromacs 4.5.x works only with OpenMM 2.x. You might be able to use CUDA 4.0, but you will probably have to recompile OpenMM from source. Cheers, -- Szilárd On Fri, Aug 19, 2011 at 2:23 AM, Park, Jae Hyun nmn pa...@ornl.gov wrote: Dear GMX users, I am installing GMX 4.5.3 with GPU. But, the CUDA in my GPU machine is ver 4.0. Can I use this version of CUDA and openmm-3.1.1? Or, do I have to re-install CUDA 3.2 and openmm-2.0 as described in manual? Thank you in advance for your kind instruction. Jae H. Park === Jae Hyun Park, Ph. D. Physics Division Oak Ridge National Laboratory PO. Box 2008, MS-6372 Oak Ridge, TN 37831 Phone (865) 241-1482 E-mail pa...@ornl.gov -- 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
