Re: [gmx-users] About Compiler Compatibility for Gromacs 4.6.2 Compilation
On Nov 10, 2013 10:04 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Yes (unless you are using AMD cpus), per the installation instructions, although you will probably do slightly better with GCC 4.7, and should not do a new install of 4.6.2 after 4.6.3 is released. In particular, 4.6.2 has an affinity-related performance regression when using external MPI libraries. Mark On Nov 10, 2013 7:55 AM, vidhya sankar scvsankar_...@yahoo.com wrote: Dear Justin and Mark Thank you for your Previous reply Can i Use the Following Intel Compiler for grmacs 4.6.2 in centos Linux OS ? Intel® C++ Composer XE 2013 for Linux it Includes Intel® C++ Compiler, Intel® Integrated Performance Primitives 7.1, Intel® Math Kernel Library 11.0, Intel Cilk™ Plus, the Intel® Threading Building Blocks (Intel® TBB)” -- 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: mdrun on 8-core AMD + GTX TITAN (was: Re: [gmx-users] Re: Gromacs-4.6 on two Titans GPUs)
On Sun, Nov 10, 2013 at 5:28 AM, Dwey Kauffman mpi...@gmail.com wrote: Hi Szilard, Thank you very much for your suggestions. Actually, I was jumping to conclusions too early, as you mentioned AMD cluster, I assumed you must have 12-16-core Opteron CPUs. If you have an 8-core (desktop?) AMD CPU, than you may not need to run more than one rank per GPU. Yes, we do have independent clusters of AMD, AMD opteron, Intel Corei7. All nodes of three clusters are installed with (at least) 1 GPU card. I have run the same test on these three clusters. Let's focus on a basic scaling issue: One GPU v.s Two GPUs within the same node of 8-core AMD cpu. Using 1 GPU, we can have a performance of ~32 ns/day. Using two GPU, we gain not much more ( ~38.5 ns/day ). It is about ~20% more performance. However, this is not really true because in some tests, I also saw only 2-5% more, which really surprised me. Neither run had a PP-PME work distribution suitable for the hardware it was running on (and fixing that for each run requires opposite changes). Adding a GPU and hoping to see scaling requires that there be proportionately more GPU work available to do, *and* enough absolute work to do. mdrun tries to do this, and reports early in the log file, which is one of the reasons Szilard asked to see whole log files - please use a file sharing service to do that. As you can see, this test was made on the same node regardless of networking. Can the performance be improved say 50% more when 2 GPUs are used on a general task ? If yes, how ? Indeed, as Richard pointed out, I was asking for *full* logs, these summaries can't tell much, the table above the summary entitled R E A L C Y C L E A N D T I M E A C C O U N T I N G as well as other reported information across the log file is what I need to make an assessment of your simulations' performance. Please see below. However, in your case I suspect that the bottleneck is multi-threaded scaling on the AMD CPUs and you should probably decrease the number of threads per MPI rank and share GPUs between 2-4 ranks. After I test all three clusters, I found it may NOT be an issue of AMD cpus. Intel cpus has the SAME scaling issue. However, I am curious as to how you justify the setup of 2-4 ranks sharing GPUs ? Can you please explain it a bit more ? NUMA effects on multi-socket AMD processors are particularly severe; the way GROMACS uses OpenMP is not well suited to them. Using a rank (or two) per socket will greatly reduce those effects, but introduces different algorithmic overhead from the need to do DD and explicitly communicate between ranks. (You can see the latter in your .log file snippets below.) Also, that means the parcel of PP work available from a rank to give to the GPU is smaller, which is the opposite of what you'd like for GPU performance and/or scaling. We are working on a general solution for this and lots of related issues in the post-5.0 space, but there is a very hard limitation imposed by the need to amortize the cost of CPU-GPU transfer by having lots of PP work available to do. You could try running mpirun -np 4 mdrun -ntomp 2 -gpu_id 0011 but I suspect this won't help because your scaling issue Your guess is correct but why is that ? it is worse. The more nodes are involved in a task, the performance is worse. in my experience even reaction field runs don't scale across nodes with 10G ethernet if you have more than 4-6 ranks per node trying to communicate (let alone with PME). What dose it mean let alone with PME ? how to do so ? by mdrun ? I do know mdrun -npme to specify PME process. If using PME (rather than RF), network demands are more severe. Thank you. Dwey ### One GPU R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Th. Count Wall t (s) G-Cycles % - Neighbor search18 11 431.81713863.390 1.6 Launch GPU ops.18501 472.90615182.556 1.7 Force 185011328.61142654.785 4.9 PME mesh 18501 11561.327 371174.09042.8 Wait GPU local 185016888.008 221138.11125.5 NB X/F buffer ops. 189911216.49939055.455 4.5 Write traj.18 1030 12.741 409.039 0.0 Update 185011696.35854461.226 6.3 Constraints185011969.72663237.647 7.3 Rest 11458.82046835.133 5.4 - Total 1 27036.812 868011.431 100.0
[gmx-users] Umbrella Sampling tutorial
Dear Justin Thanks for your reply. You are right. I should not extrapolate too literally from your tutorial to my system. But, I have a general question: There is 2 groups in COM pulling method (reference group + pull group). If I want to use pull_geometry = distance, so, I should fix reference group to be immobile. Is it true? On the other hand, I want to know exactly using position restraining on reference group is optional or mandatory in COM pulling method? Best wishes -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: choosing force field
Thank you Justin for your kind help. The simple reason for considering only gromos parameter sets is that the parameters for the metal ions (in my protein) are not defined in other force fields. On Sat, Nov 9, 2013 at 7:18 PM, Justin Lemkul [via GROMACS] ml-node+s5086n5012376...@n6.nabble.com wrote: On 11/9/13 12:48 AM, pratibha wrote: Sorry for the previous mistake. Instead of 53a7, the force field which I used was 53a6. 53A6 is known to under-stabilize helices, so if a helix did not appear in a simulation using this force field, it is not definitive proof that the structure does not populate helical structures. I generally see mixed opinions in the literature in terms of which Gromos parameter set is the most reliable. As was asked by someone else, is there a reason you are only considering Gromos parameter sets? Others may be better suited to your study. -Justin On Fri, Nov 8, 2013 at 12:10 AM, Justin Lemkul [via GROMACS] [hidden email] http://user/SendEmail.jtp?type=nodenode=5012376i=0 wrote: On 11/7/13 12:14 PM, pratibha wrote: My protein contains metal ions which are parameterized only in gromos force field. Since I am a newbie to MD simulations, it would be difficult for me to parameterize those myself. Can you please guide me as per my previous mail which out of the two simulations should I consider more reliable-43a1 or 53a7? AFAIK, there is no such thing as 53A7, and your original message was full of similar typos, making it nearly impossible to figure out what you were actually doing. Can you indicate the actual force field(s) that you have been using in case someone has any ideas? The difference between 53A6 and 54A7 should be quite pronounced, in my experience, thus any guesses as to what 53A7 should be doing are not productive because I don't know what that is. -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 [hidden email] http://user/SendEmail.jtp?type=nodenode=5012325i=0 | (410) 706-7441 == -- gmx-users mailing list[hidden email] http://user/SendEmail.jtp?type=nodenode=5012325i=1 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 [hidden email] http://user/SendEmail.jtp?type=nodenode=5012325i=2. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- If you reply to this email, your message will be added to the discussion below: . NAML http://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml -- View this message in context: http://gromacs.5086.x6.nabble.com/choosing-force-field-tp5012242p5012370.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- == 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 [hidden email] http://user/SendEmail.jtp?type=nodenode=5012376i=1 | (410) 706-7441 == -- gmx-users mailing list[hidden email]http://user/SendEmail.jtp?type=nodenode=5012376i=2 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 [hidden email]http://user/SendEmail.jtp?type=nodenode=5012376i=3. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/choosing-force-field-tp5012242p5012376.html To unsubscribe from choosing force field, click herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=5012242code=a2Fwb29ycHJhdGliaGE3QGdtYWlsLmNvbXw1MDEyMjQyfC02NjkwNjY5MjU= .
[gmx-users] problem in running mdrun command
Dear all I encounter a problem while running command mdrun_mpi -v -deffnm em in gromacs. I am new to the gromacs. i just ran test calculation, *simulation of lyzozyme in water*. i am able to generate gro, tpr files. But in the final step i got following error. Thanks in advance. [localhost.localdomain:23122] mca: base: component_find: paffinity mca_paffinity_linux uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23123] mca: base: component_find: paffinity mca_paffinity_linux uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23123] mca: base: component_find: ras mca_ras_dash_host uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23123] mca: base: component_find: ras mca_ras_gridengine uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23123] mca: base: component_find: ras mca_ras_localhost uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23123] mca: base: component_find: errmgr mca_errmgr_hnp uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23123] mca: base: component_find: errmgr mca_errmgr_orted uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23123] mca: base: component_find: errmgr mca_errmgr_proxy uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23123] mca: base: component_find: iof mca_iof_proxy uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23123] mca: base: component_find: iof mca_iof_svc uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23122] mca: base: component_find: rcache mca_rcache_rb uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost:23122] *** Process received signal *** [localhost:23122] Signal: Segmentation fault (11) [localhost:23122] Signal code: Address not mapped (1) [localhost:23122] Failing at address: 0x4498 [localhost:23122] [ 0] /lib64/libpthread.so.0() [0x3fcee0f500] [localhost:23122] [ 1] /usr/local/lib/libmpi.so.1(PMPI_Comm_size+0x4e) [0x2acc6d93727e] [localhost:23122] [ 2] /usr/local/gromacs/bin/../lib/libgmx_mpi.so.8(gmx_setup+0x32) [0x2acc6d195e02] [localhost:23122] [ 3] /usr/local/gromacs/bin/../lib/libgmx_mpi.so.8(init_par+0x51) [0x2acc6d234251] [localhost:23122] [ 4] mdrun_mpi(cmain+0x11f9) [0x435799] [localhost:23122] [ 5] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3fcea1ecdd] [localhost:23122] [ 6] mdrun_mpi() [0x406ee9] [localhost:23122] *** End of error message *** Segmentation fault (core dumped) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_analyze
On 11/10/13 12:20 AM, bharat gupta wrote: Hi, I used the command g_hbond to find h-bond between residues 115-118 and water. Then I used g_analyze to find out the average and it gives the value for the hbonds like this :- std. dev.relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 6.877249e-02 2.546419e-01 5.092839e-03 2.1813.495 SS2 6.997201e-02 2.673450e-01 5.346901e-03 2.4215.001 When I calculated the average manually, by taking the average of numbers in second column of hbnum.xvg file, I got a value of around 13.5.. What is the reason for such a large difference. Hard to say, but I've never known g_analyze to be wrong, so I'd suspect something is amiss in your manual calculation. The difference between 13.5 and 0.0069 is huge; you should be able to scan through the data file to see what the expected value should be. In another case, g_analyze gives avg values of aroun 6.9 for hbond between two residues and when I calculated it maually I got the avg values as 6.8 .. Whats the meaning of SS1 and SS2,?? Does it mean that SS1 refers to time and SS2 refers to hbond numbers in the hbnum.xvg obtained from g_hbond analysis ?? Data sets 1 and 2. You will note that there are two columns of data in the -hbnum output produced by g_hbond, with titles explaining both. -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] Umbrella Sampling tutorial
On 11/10/13 5:31 AM, shahab shariati wrote: Dear Justin Thanks for your reply. You are right. I should not extrapolate too literally from your tutorial to my system. But, I have a general question: There is 2 groups in COM pulling method (reference group + pull group). If I want to use pull_geometry = distance, so, I should fix reference group to be immobile. Is it true? What you described earlier should not be attempted with distance geometry. It won't work very well. The use of restraints is almost NEVER necessary, especially in the case where the reference group is much more massive than the pulling group. On the other hand, I want to know exactly using position restraining on reference group is optional or mandatory in COM pulling method? Almost never used. More explicitly - you do not need position restraints. -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] problem in running mdrun command
Hi, There's nothing GROMACS-specific here - something about your MPI installation, configuration or use is pretty wrong, but we can't help work out what. Mark On Sun, Nov 10, 2013 at 12:31 PM, S.Chandra Shekar chandrashe...@iisertvm.ac.in wrote: Dear all I encounter a problem while running command mdrun_mpi -v -deffnm em in gromacs. I am new to the gromacs. i just ran test calculation, *simulation of lyzozyme in water*. i am able to generate gro, tpr files. But in the final step i got following error. Thanks in advance. [localhost.localdomain:23122] mca: base: component_find: paffinity mca_paffinity_linux uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23123] mca: base: component_find: paffinity mca_paffinity_linux uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23123] mca: base: component_find: ras mca_ras_dash_host uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23123] mca: base: component_find: ras mca_ras_gridengine uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23123] mca: base: component_find: ras mca_ras_localhost uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23123] mca: base: component_find: errmgr mca_errmgr_hnp uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23123] mca: base: component_find: errmgr mca_errmgr_orted uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23123] mca: base: component_find: errmgr mca_errmgr_proxy uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23123] mca: base: component_find: iof mca_iof_proxy uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23123] mca: base: component_find: iof mca_iof_svc uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23122] mca: base: component_find: rcache mca_rcache_rb uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost:23122] *** Process received signal *** [localhost:23122] Signal: Segmentation fault (11) [localhost:23122] Signal code: Address not mapped (1) [localhost:23122] Failing at address: 0x4498 [localhost:23122] [ 0] /lib64/libpthread.so.0() [0x3fcee0f500] [localhost:23122] [ 1] /usr/local/lib/libmpi.so.1(PMPI_Comm_size+0x4e) [0x2acc6d93727e] [localhost:23122] [ 2] /usr/local/gromacs/bin/../lib/libgmx_mpi.so.8(gmx_setup+0x32) [0x2acc6d195e02] [localhost:23122] [ 3] /usr/local/gromacs/bin/../lib/libgmx_mpi.so.8(init_par+0x51) [0x2acc6d234251] [localhost:23122] [ 4] mdrun_mpi(cmain+0x11f9) [0x435799] [localhost:23122] [ 5] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3fcea1ecdd] [localhost:23122] [ 6] mdrun_mpi() [0x406ee9] [localhost:23122] *** End of error message *** Segmentation fault (core dumped) -- 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] Umbrella Sampling tutorial
Dear Justin Very thanks for your reply. What you described earlier should not be attempted with distance geometry. It won't work very well. The use of restraints is almost NEVER necessary, especially in the case where the reference group is much more massive than the pulling group. I want to calculate Potential of mean force as a function of the distance between the centers of mass of drug and the lipid bilayer. You said distance geometry won't work very well in my case. What is your better suggestion about my case? Best wishes -- 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] Umbrella Sampling tutorial
On 11/10/13 9:14 AM, shahab shariati wrote: Dear Justin Very thanks for your reply. What you described earlier should not be attempted with distance geometry. It won't work very well. The use of restraints is almost NEVER necessary, especially in the case where the reference group is much more massive than the pulling group. I want to calculate Potential of mean force as a function of the distance between the centers of mass of drug and the lipid bilayer. You said distance geometry won't work very well in my case. What is your better suggestion about my case? http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05a_pull_tips.html pull_geometry = position -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] Bilayer COM removal issue: Large VCM
Hi All, I am experiencing a few problems in membrane simulations wrt COM removal. I downloaded a 400 ns pre-equilibrated Slipid-DMPC membrane with all the accompanying files. I then carried out the following steps: 1) energy minimization 2) NVT Eq - 100 ps 3) NPT Eq - 250 ps (Berendsen temp, Pres coupling) Then I used g_select to select the upper and lower DMPC leaflets. The then carried out a 250 ps NPT eq again. The only change was: comm-grps= SOL DMPC ==comm-grps = SOL upper lower On every step in log file, I get the following message: *Step Time Lambda 124000 248.00.0Large VCM(group lower): -0.00051, -0.00515, -0.00652, Temp-cm: 8.11828e+29 Energies (kJ/mol)U-BProper Dih. Improper Dih. LJ-14 Coulomb-147.23818e+044.19778e+046.46641e+024.54801e+03 -1.45245e+05LJ (SR)LJ (LR) Disper. corr. Coulomb (SR) Coul. recip.2.79689e+04 -3.78407e+03 -2.10679e+03 -5.84134e+05 -8.87497e+04 PotentialKinetic En. Total EnergyTemperature Pres. DC (bar) -6.76497e+051.76468e+05 -5.00029e+05 3.10424e+02 -1.05704e+02 Pressure (bar) Constr. rmsd -1.85927e+02 6.42934e-06* *Large VCM(group lower): -0.00187, -0.00369, 0.00032, Temp-cm: 2.02076e+29Large VCM(group lower): -0.00725, -0.00278, -0.00549, Temp-cm: 1.05988e+30Large VCM(group lower): 0.00020, 0.00308, -0.00176, Temp-cm: 1.48126e+29Large VCM(group lower): -0.00541, 0.00546, -0.00166, Temp-cm: 7.24656e+29Large VCM(group lower): -0.00220, 0.00362, -0.00741, Temp-cm: 8.53812e+29Large VCM(group lower): 0.00140, -0.00160, 0.00029, Temp-cm: 5.39679e+28Large VCM(group lower): -0.00056, -0.00293, -0.00364, Temp-cm: 2.59422e+29Large VCM(group lower): -0.00172, -0.00260, 0.00494, Temp-cm: 3.99945e+29Large VCM(group lower): 0.00252, 0.00594, 0.00068, Temp-cm: 4.93342e+29* *DD step 124999 vol min/aver 0.702 load imb.: force 1.3% pme mesh/force 0.636* I do not know what to make of it. There are no issues when I remove COM for the entire system. I have seen this issue come up a few times in the archives too, but I didn't find a satisfactory solution since the bilayer was very well equilibrated. I would appreciate any suggestions. Thank you. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_analyze
I checked the file hbnum.xvg file and it contains three columns - time, hbonds, hbonds that donot follow the angle criteria. In that case SS1 is the average of actual hbonds (2nd column ) and SS2 is the average of 3rd column. Am I right here or not ?? I tried to calculate the h-bond for residues 115-118 individually, and then checked the average for each residue. For single residue calculation, the g_analyze average value is correct. But when I calculate the h-bond as a range 115-118, I get the g_analyze value as 1.62 . I calculated the average manually in excel, got the average values as 16.2 [which is (g_analyze avg value)/10]. I then added up the average values of h-bonds of individual residues and the final comes around 16.2, same as that of the 115-118 range h-bonds. This means that my calculation is correct. I also used trjorder to calculate h-bond at distance 0.34 for residues 115-118. I got the average value around 2.51 from g_analyze, where as manual calculation gives 25.1. I don't knw why for the range the g_analyze give avg as (actual avg value)/10 ?? Why does trjorder and g_hbond gives different number of hydrogen bonds for the same residue set?? Thanks --- BHARAT On Sun, Nov 10, 2013 at 10:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/10/13 12:20 AM, bharat gupta wrote: Hi, I used the command g_hbond to find h-bond between residues 115-118 and water. Then I used g_analyze to find out the average and it gives the value for the hbonds like this :- std. dev.relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 6.877249e-02 2.546419e-01 5.092839e-03 2.1813.495 SS2 6.997201e-02 2.673450e-01 5.346901e-03 2.4215.001 When I calculated the average manually, by taking the average of numbers in second column of hbnum.xvg file, I got a value of around 13.5.. What is the reason for such a large difference. Hard to say, but I've never known g_analyze to be wrong, so I'd suspect something is amiss in your manual calculation. The difference between 13.5 and 0.0069 is huge; you should be able to scan through the data file to see what the expected value should be. In another case, g_analyze gives avg values of aroun 6.9 for hbond between two residues and when I calculated it maually I got the avg values as 6.8 .. Whats the meaning of SS1 and SS2,?? Does it mean that SS1 refers to time and SS2 refers to hbond numbers in the hbnum.xvg obtained from g_hbond analysis ?? Data sets 1 and 2. You will note that there are two columns of data in the -hbnum output produced by g_hbond, with titles explaining both. -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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Thankful
Justin, thank you very much for your kind help about LIE and PME Williams -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_analyze
On 11/10/13 7:18 PM, bharat gupta wrote: I checked the file hbnum.xvg file and it contains three columns - time, hbonds, hbonds that donot follow the angle criteria. In that case SS1 is The third column is not actually H-bonds, then ;) the average of actual hbonds (2nd column ) and SS2 is the average of 3rd column. Am I right here or not ?? Yes. I tried to calculate the h-bond for residues 115-118 individually, and then checked the average for each residue. For single residue calculation, the g_analyze average value is correct. But when I calculate the h-bond as a range 115-118, I get the g_analyze value as 1.62 . I calculated the average manually in excel, got the average values as 16.2 [which is (g_analyze avg value)/10]. That is impossible. You cannot get a different average by examining the same numbers. Read the g_analyze output again - I am willing to bet that you're not seeing the exponent of the scientific notation. I then added up the average values of h-bonds of individual residues and the final comes around 16.2, same as that of the 115-118 range h-bonds. This means that my calculation is correct. I also used trjorder to calculate h-bond at distance 0.34 for residues 115-118. I got the average value around 2.51 from g_analyze, where as manual calculation gives 25.1. I don't knw why for the range the g_analyze give avg as (actual avg value)/10 ?? Why does trjorder and g_hbond gives different number of hydrogen bonds for the same residue set?? All of this comes down to correctly reading the screen output. I have no idea what you're doing with trjorder, though. It doesn't measure H-bonds. -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] Re: g_analyze
Thanks for your reply. I was missing the scientific notation part. Now everything is fine. Regarding trjorder, it doesn't measure h-bonds but gives the water nearest to protein. On Mon, Nov 11, 2013 at 10:12 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/10/13 7:18 PM, bharat gupta wrote: I checked the file hbnum.xvg file and it contains three columns - time, hbonds, hbonds that donot follow the angle criteria. In that case SS1 is The third column is not actually H-bonds, then ;) the average of actual hbonds (2nd column ) and SS2 is the average of 3rd column. Am I right here or not ?? Yes. I tried to calculate the h-bond for residues 115-118 individually, and then checked the average for each residue. For single residue calculation, the g_analyze average value is correct. But when I calculate the h-bond as a range 115-118, I get the g_analyze value as 1.62 . I calculated the average manually in excel, got the average values as 16.2 [which is (g_analyze avg value)/10]. That is impossible. You cannot get a different average by examining the same numbers. Read the g_analyze output again - I am willing to bet that you're not seeing the exponent of the scientific notation. I then added up the average values of h-bonds of individual residues and the final comes around 16.2, same as that of the 115-118 range h-bonds. This means that my calculation is correct. I also used trjorder to calculate h-bond at distance 0.34 for residues 115-118. I got the average value around 2.51 from g_analyze, where as manual calculation gives 25.1. I don't knw why for the range the g_analyze give avg as (actual avg value)/10 ?? Why does trjorder and g_hbond gives different number of hydrogen bonds for the same residue set?? All of this comes down to correctly reading the screen output. I have no idea what you're doing with trjorder, though. It doesn't measure H-bonds. -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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_analyze
On 11/10/13 8:30 PM, bharat gupta wrote: Thanks for your reply. I was missing the scientific notation part. Now everything is fine. Regarding trjorder, it doesn't measure h-bonds but gives the water nearest to protein. I wouldn't try to draw any sort of comparison between the output of trjorder and g_hbond. If you want to measure H-bonds, there's only one tool for that. -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] Re: g_analyze
But trjorder can be used to calculate the hydration layer or shell around residues ... Right ?? On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/10/13 8:30 PM, bharat gupta wrote: Thanks for your reply. I was missing the scientific notation part. Now everything is fine. Regarding trjorder, it doesn't measure h-bonds but gives the water nearest to protein. I wouldn't try to draw any sort of comparison between the output of trjorder and g_hbond. If you want to measure H-bonds, there's only one tool for that. -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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_analyze
On 11/10/13 8:38 PM, bharat gupta wrote: But trjorder can be used to calculate the hydration layer or shell around residues ... Right ?? Yes, but I also tend to think that integrating an RDF is also a more straightforward way of doing that. With trjorder, you set some arbitrary cutoff that may or may not be an informed decision - with an RDF it is clear where the hydration layers are. -Justin On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/10/13 8:30 PM, bharat gupta wrote: Thanks for your reply. I was missing the scientific notation part. Now everything is fine. Regarding trjorder, it doesn't measure h-bonds but gives the water nearest to protein. I wouldn't try to draw any sort of comparison between the output of trjorder and g_hbond. If you want to measure H-bonds, there's only one tool for that. -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 -- == 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] Re: g_analyze
thank you informing about g_rdf... Is it possible to dump the structure with those average water molecules interacting with the residues. I generated the hbond.log file which gives the details but I need to generate a figure for this ?? On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/10/13 8:38 PM, bharat gupta wrote: But trjorder can be used to calculate the hydration layer or shell around residues ... Right ?? Yes, but I also tend to think that integrating an RDF is also a more straightforward way of doing that. With trjorder, you set some arbitrary cutoff that may or may not be an informed decision - with an RDF it is clear where the hydration layers are. -Justin On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/10/13 8:30 PM, bharat gupta wrote: Thanks for your reply. I was missing the scientific notation part. Now everything is fine. Regarding trjorder, it doesn't measure h-bonds but gives the water nearest to protein. I wouldn't try to draw any sort of comparison between the output of trjorder and g_hbond. If you want to measure H-bonds, there's only one tool for that. -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 -- == 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 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
