[gmx-users] how to optimize performance of IBM Power 775?
Dear: Our institute got a IBM Power 775 cluster and it claimed to be very good. However, it doesn't support g_tune_pme. I use the following script for job submission: #@ job_name = gromacs_job #@ output = gromacs.out #@ error = gromacs.err #@ class = kdm #@ node = 4 #@ tasks_per_node = 32 #@ wall_clock_limit = 01:00:00 #@ network.MPI = sn_all,not_shared,US,HIGH #@ notification = never #@ environment = COPY_ALL #@ job_type = parallel #@ queue mpiexec -n 128 /opt/gromacs/4.5.5/bin/mdrun -nosum -dlb yes -v -s md.tpr it is only 7 ns/day. However, in another cluster with the same system, Core number and parameters, I can get up to 30 ns/day. Does anybody have any advices for this issue? thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Topology- make bonds with certain cut-off distance
Hi all, I want build a toplogy for a protein , for which , each and every atom has to make bonds with other atoms with in certain specified cut-off distance. How can i do this ? Please suggest me a way, Thanks in advance, Mohan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_tune_pme optimal PME nodes for multiple nodes
Dear gmx users, I am using 4.5.5 of gromacs. I was trying to use g_tune_pme for a simulation. I intend to execute mdrun at multiple nodes with 12 cores each. Therefore, I would like to optimize the number of pme nodes. I could execute g_tune_pme -np 12 md.tpr. But this will only find the optimal PME nodes for single nodes run. How do I find the optimal PME nodes for multiple nodes. Any suggestion would be helpful. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Force fields, is there a review article?
I have read a variation on this advice many. many times here: The ultimate choice of force field should be based on your reading and understanding of their derivation and known applications/limitations, all of which comes from the literature. Choose the one that you think is most sound :) I am probably not the only person here who is attempting to learn and use molecular dynamics software for the first time. I am probably not the only person here who is trying to simulate a molecule for which there is NO published molecular dynamics study. Sure, it's a protein in water. Is that enough to tell me which force field(s) will give me a representative result, or not? I search through abstracts in molecular dynamics at the library, but I never seem to find articles which are general enough. It would be very helpful if someone more knowledgeable in the field could point us newcomers at a review article, even a somewhat dated one, which surveys the use and utility of a few different force fields. It would be a good starting point. Thanks! -- View this message in context: http://gromacs.5086.n6.nabble.com/Force-fields-is-there-a-review-article-tp5000519.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology- make bonds with certain cut-off distance
Hi, In case you want the bonds to be dynamic I think the only way is to use tabulated interactions. A bit tedious to set up, but doable. Note that this will NOT emulate angles or dihedrals, just the stretching term. I can't understand why you would want bonds between all atoms within a certain distance, however, and I hope you know what you're doing. Erik 25 aug 2012 kl. 06.54 skrev mohan maruthi sena: Hi all, I want build a toplogy for a protein , for which , each and every atom has to make bonds with other atoms with in certain specified cut-off distance. How can i do this ? Please suggest me a way, Thanks in advance, Mohan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Force fields, is there a review article?
I have read a variation on this advice many. many times here: The ultimate choice of force field should be based on your reading and understanding of their derivation and known applications/limitations, all of which comes from the literature. Choose the one that you think is most sound :) I am probably not the only person here who is attempting to learn and use molecular dynamics software for the first time. I am probably not the only person here who is trying to simulate a molecule for which there is NO published molecular dynamics study. Sure, it's a protein in water. Is that enough to tell me which force field(s) will give me a representative result, or not? maybe one of the best thing to do is to test the FF vs experimental data and check which one reproduces them better or provides more stability. a recent example, a bit oriented toward a particular field of research but interested in terms of methodology used is the following one by David Case: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2997720/. this sentence explains you why:The high resolution of the diffraction data (0.96Å) and the simplicity of the crystallization solution (nearly pure water) makes it possible to attribute any inconsistencies between the crystal structure and our simulations to artifacts of the models rather than inadequate representation of the crystal environment or uncertainty in the experiment.. it's not a problem of how it sounds, but if it works in sense of reproducing exprimental data, indeed. being a person that works in the world of NMR, I am always interested in FF that are tested against experimental data in my field, so this paper is interesting too: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905107/?tool=pmcentrez. like many papers written by Raphael Bruschweiler (like this: http://spin.magnet.fsu.edu/pubs/li_g28-g8_jctc2011.pdf). this one is relevant for AMBER FF lovers (like me) but also because it enters a bit in depth in the details of the delicate but necessary operation of improving a FF (a thing we experimentalists that use MD always have to trust but, I think, with a careful and critical eye kept on the problem): http://www.ncbi.nlm.nih.gov/pubmed/16981200. water is crytical too, a bit is written in the David Case paper I have cited but even more can be found in literature (I am not an expert in this topics). maybe someone else in the ML can be more helpful than me about this. I search through abstracts in molecular dynamics at the library, but I never seem to find articles which are general enough. It would be very helpful if someone more knowledgeable in the field could point us newcomers at a review article, even a somewhat dated one, which surveys the use and utility of a few different force fields. It would be a good starting point. this one seems to be a thing of the kind you are looking for, but I don't know it even though it seems interesting (just found googling the title of other papers I have just listed): http://maxwell.uncc.edu/abaumket/phys6203_files/Reading/force-fields.pdf Regards. L -- Luca Mollica Protein Dynamics and Flexibility by NMR Institut de Biologie Structurale Jean-Pierre Ebel UMR 5075 CNRS/CEA/UJF 41 rue Jules Horowitz 38027 Grenoble Cedex 01 E-mail: luca.moll...@ibs.fr lucamollica...@gmail.com Skype:lucamollica Linkedin: http://fr.linkedin.com/in/lucamollica Tel: +33.(0)438783889 Fax: +33.(0)438785494 We need not destroy the past. It is gone. (J.Cage) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] User specified potential functions
Dear Uses: I am using User specified potential functions with Gromacs-4.5.4. According to the manual, I wrote a FORTRAN program to generate the table.xvg file. When I ran mdrun, the error came out as below: .. Only 7 columns on line 4199 in file table.xvg Only 7 columns on line 4200 in file table.xvg Only 7 columns on line 4201 in file table.xvg --- Program mdrun_mpi, VERSION 4.5.4 Source code file: /home/wxm/gromacs-4.5.4/src/mdlib/tables.c, line: 366 Fatal error: Trying to read file table.xvg, but nr columns = 8, should be 7 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors It says I have 8 column in the table.xvg file, while the right number is 7. I checked the table.xvg file and it is 7 column. When the original table.xvg file in GMXLIB directory is used, the same error came out too. Part of the table.xvg file is below: .. 3.001425E-03 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 3.501662E-03 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 4.001900E-03 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 4.502137E-03 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 5.002375E-03 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 5.502612E-03 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 6.002850E-03 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 6.503087E-03 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 .. 4.702232E-02 2.1276594734E+01 4.5269348348E+02 9.2771104806E+07 1.1843119200E+10 8.6064778870E+15 2.1973985051E+18 4.752256E-02 2.1052630579E+01 4.4321325430E+02 8.7063920276E+07 1.0997547302E+10 7.5801262138E+15 1.9149791631E+18 4.802280E-02 2.082344E+01 4.3402773655E+02 8.1762178037E+07 1.0220271769E+10 6.6850537574E+15 1.6712633600E+18 4.852304E-02 2.0618555722E+01 4.2512484005E+02 7.6833292574E+07 9.5051491454E+09 5.9033548478E+15 1.4606238105E+18 4.902327E-02 2.0408162296E+01 4.1649308830E+02 7.2247595220E+07 8.8466438924E+09 5.2197150150E+15 1.2782974940E+18 4.952351E-02 2.0202019242E+01 4.0812158147E+02 6.7978046910E+07 8.2397628705E+09 4.6210148617E+15 1.1202459739E+18 5.002375E-02 1.999050E+01 3.996200E+02 6.381761E+07 7.6799974465E+09 4.0959976654E+15 9.8303939301E+17 Any suggestions are welcome! Thank you in advance! 2012-08-25 toby1024 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Topology- make bonds with certain cut-off distance
Hi , Thanks for your reply. I actually want to build an elastic network model (ENM) for Protein containing 372 residues. According to literature, ENM model only considers C-alpha atoms of protein and discards rest of the atoms.The potential only considers bonded term only. It does not contain angle,dihedral or non-bonded term. To build an ENM model the specified atom makes bond with all other atoms with certain cutoff distance. I consider the distance between two c-alpha atoms is 0.38nm and force constant of 69.1 kj/(nm)2.I have written a code which gives the number of atoms around a particular atom with in certain cut-off distance, With this i will know what are the atoms that are needed to connect a particular atom.I have generated .gro and .top files using pdb2gmx command . After generating topology file , I replace bonds section with the connectivity information i get from code. The next steps are equilibration and production. I am not sure whether it takes connectivity information from topology or not. If it is not then how can i mention it forms bonds with in certain distance . Finally , if i run the simulation with all the above mentioned steps and load the trajectory in vmd , the protien gets contracted after first step. Thanks, Mohan On Sat, Aug 25, 2012 at 3:43 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, In case you want the bonds to be dynamic I think the only way is to use tabulated interactions. A bit tedious to set up, but doable. Note that this will NOT emulate angles or dihedrals, just the stretching term. I can't understand why you would want bonds between all atoms within a certain distance, however, and I hope you know what you're doing. Erik 25 aug 2012 kl. 06.54 skrev mohan maruthi sena: Hi all, I want build a toplogy for a protein , for which , each and every atom has to make bonds with other atoms with in certain specified cut-off distance. How can i do this ? Please suggest me a way, Thanks in advance, Mohan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Error:The selected GPU (#0, Tesla M2090) is not supported by Gromacs!
Dear all, I got the following error while running mdrun-gpu, I got the following error: The selected GPU (#0, Tesla M2090) is not supported by Gromacs! Although in the Gromacs site , it says that Tesla M2090 is supported. Then, I have used mdrun-gpu -device OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes -s imd.tpr command. I got the following warning and I am using this for calculating GB-polarization energy, but the result does not contains GB-polarization energy at all. WARNING: Non-supported GPU selected (#0, Tesla M2090), forced continuing.Note, that the simulation can be slow or it migth even crash. Started mdrun on node 0 Sat Aug 25 00:04:18 2012 Step Time Lambda 00.00.0 Energies (kJ/mol) PotentialKinetic En. Total EnergyTemperature -2.22432e+050.0e+00 -2.22432e+050.0e+00 If anyone has ever experienced this kind of problem, or knows the solution, please let me know. Thanks in advance. Thanks, Jesmin -- Jesmin Jahan Tithi PhD Student, CS Stony Brook University, NY-11790. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error:The selected GPU (#0, Tesla M2090) is not supported by Gromacs!
On 8/25/12 10:57 AM, jesmin jahan wrote: Dear all, I got the following error while running mdrun-gpu, I got the following error: The selected GPU (#0, Tesla M2090) is not supported by Gromacs! Although in the Gromacs site , it says that Tesla M2090 is supported. Then, I have used mdrun-gpu -device OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes -s imd.tpr command. I got the following warning and I am using this for calculating GB-polarization energy, but the result does not contains GB-polarization energy at all. WARNING: Non-supported GPU selected (#0, Tesla M2090), forced continuing.Note, that the simulation can be slow or it migth even crash. Started mdrun on node 0 Sat Aug 25 00:04:18 2012 Step Time Lambda 00.00.0 Energies (kJ/mol) PotentialKinetic En. Total EnergyTemperature -2.22432e+050.0e+00 -2.22432e+050.0e+00 If anyone has ever experienced this kind of problem, or knows the solution, please let me know. Thanks in advance. The list is simply outdated and will be updated in the next version. Your command line (using force-device=yes) is the only workaround. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error:The selected GPU (#0, Tesla M2090) is not supported by Gromacs!
Hi Justin, Thanks for your reply. Do you mean that Gromacs does not support tesla M2090? I have used the force-device=yes option. But the problem is, it runs but does not give me GB-polarization energy, It only gives the the potential energy. I intention was to calculate the GB-Energy. In .mdp file I added constraints = none integrator = md pbc = no dt = 0.001 ; ps nsteps = 0 ; 10 ps = 100 ns rcoulomb= 1 rvdw= 1 rlist =1 nstgbradii = 1 rgbradii= 1 implicit_solvent= GBSA gb_algorithm= OBC ; Still sa_algorithm= None Thanks, Jesmin On Sat, Aug 25, 2012 at 11:25 AM, Justin Lemkul jalem...@vt.edu wrote: On 8/25/12 10:57 AM, jesmin jahan wrote: Dear all, I got the following error while running mdrun-gpu, I got the following error: The selected GPU (#0, Tesla M2090) is not supported by Gromacs! Although in the Gromacs site , it says that Tesla M2090 is supported. Then, I have used mdrun-gpu -device OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes -s imd.tpr command. I got the following warning and I am using this for calculating GB-polarization energy, but the result does not contains GB-polarization energy at all. WARNING: Non-supported GPU selected (#0, Tesla M2090), forced continuing.Note, that the simulation can be slow or it migth even crash. Started mdrun on node 0 Sat Aug 25 00:04:18 2012 Step Time Lambda 00.00.0 Energies (kJ/mol) PotentialKinetic En. Total EnergyTemperature -2.22432e+050.0e+00 -2.22432e+050.0e+00 If anyone has ever experienced this kind of problem, or knows the solution, please let me know. Thanks in advance. The list is simply outdated and will be updated in the next version. Your command line (using force-device=yes) is the only workaround. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Jesmin Jahan Tithi PhD Student, CS Stony Brook University, NY-11790. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error:The selected GPU (#0, Tesla M2090) is not supported by Gromacs!
On 8/25/12 11:50 AM, jesmin jahan wrote: Hi Justin, Thanks for your reply. Do you mean that Gromacs does not support tesla M2090? I have used the force-device=yes option. But the problem is, it runs but does not give me GB-polarization energy, It only gives the the potential energy. I intention was to calculate the GB-Energy. In .mdp file I added You won't get it if you're running on GPU, unfortunately. http://redmine.gromacs.org/issues/758 -Justin constraints = none integrator = md pbc = no dt = 0.001 ; ps nsteps = 0 ; 10 ps = 100 ns rcoulomb= 1 rvdw= 1 rlist =1 nstgbradii = 1 rgbradii= 1 implicit_solvent= GBSA gb_algorithm= OBC ; Still sa_algorithm= None Thanks, Jesmin On Sat, Aug 25, 2012 at 11:25 AM, Justin Lemkul jalem...@vt.edu wrote: On 8/25/12 10:57 AM, jesmin jahan wrote: Dear all, I got the following error while running mdrun-gpu, I got the following error: The selected GPU (#0, Tesla M2090) is not supported by Gromacs! Although in the Gromacs site , it says that Tesla M2090 is supported. Then, I have used mdrun-gpu -device OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes -s imd.tpr command. I got the following warning and I am using this for calculating GB-polarization energy, but the result does not contains GB-polarization energy at all. WARNING: Non-supported GPU selected (#0, Tesla M2090), forced continuing.Note, that the simulation can be slow or it migth even crash. Started mdrun on node 0 Sat Aug 25 00:04:18 2012 Step Time Lambda 00.00.0 Energies (kJ/mol) PotentialKinetic En. Total EnergyTemperature -2.22432e+050.0e+00 -2.22432e+050.0e+00 If anyone has ever experienced this kind of problem, or knows the solution, please let me know. Thanks in advance. The list is simply outdated and will be updated in the next version. Your command line (using force-device=yes) is the only workaround. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] grompp in KALP15-DPPC
Hi, I am doing the simulation of KALP15 in DPPC following the Justin's tutorial. For the step of solvation I ran this command: # genbox -cp system.gro -cs spc216.gro -o system_solv.gro -p topol.top The output of this step is as here: Reading solute configuration frame t= 1.000 Containing 17503 atoms in 3800 residues Initialising van der waals distances... WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. Reading solvent configuration 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 4x4x4 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 13824 residues Calculating Overlap... box_margin = 0.315 Removed 10608 atoms that were outside the box Neighborsearching with a cut-off of 1.125 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 1.125 Coulomb: 1.125 LJ: 1.125 System total charge: 0.000 Grid: 18 x 18 x 18 cells Successfully made neighbourlist nri = 152829, nrj = 41861902 Checking Protein-Solvent overlap: tested 3204927 pairs, removed 30048 atoms. Checking Solvent-Solvent overlap: tested 17610 pairs, removed 60 atoms. Added 252 molecules Generated solvent containing 756 atoms in 252 residues Writing generated configuration to system_solv.gro Back Off! I just backed up system_solv.gro to ./#system_solv.gro.3# frame t= 1.000 Output configuration contains 18259 atoms in 4052 residues Volume : 272.811 (nm^3) Density : 947.87 (g/l) Number of SOL molecules: 3907 Processing topology Removing line #929 'SOL 533' from topology file (topol.top) Then running grompp for the next step ( neutralization ) grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr But the error is: Fatal error: number of coordinates in coordinate file (system_solv.gro, 18259) does not match topology (topol.top, 18159) For more information and tips for troubleshooting, please check the GROMACS Would you pleas help me? Do I need to modify the .top file before running grompp? Thanks for your suggestions in advance. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Elastic network model -gromacs
Hi all , Can any one suggest me how to build elastic network model in gromacs ( any literature,tutorial kind). Thanks in advance, K.Mohan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] grompp in KALP15-DPPC
On 8/25/12 12:26 PM, Shima Arasteh wrote: Hi, I am doing the simulation of KALP15 in DPPC following the Justin's tutorial. For the step of solvation I ran this command: # genbox -cp system.gro -cs spc216.gro -o system_solv.gro -p topol.top The output of this step is as here: Reading solute configuration frame t= 1.000 Containing 17503 atoms in 3800 residues Initialising van der waals distances... WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. Reading solvent configuration 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 4x4x4 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 13824 residues Calculating Overlap... box_margin = 0.315 Removed 10608 atoms that were outside the box Neighborsearching with a cut-off of 1.125 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 1.125 Coulomb: 1.125 LJ: 1.125 System total charge: 0.000 Grid: 18 x 18 x 18 cells Successfully made neighbourlist nri = 152829, nrj = 41861902 Checking Protein-Solvent overlap: tested 3204927 pairs, removed 30048 atoms. Checking Solvent-Solvent overlap: tested 17610 pairs, removed 60 atoms. Added 252 molecules Generated solvent containing 756 atoms in 252 residues Writing generated configuration to system_solv.gro Back Off! I just backed up system_solv.gro to ./#system_solv.gro.3# frame t= 1.000 Output configuration contains 18259 atoms in 4052 residues Volume : 272.811 (nm^3) Density: 947.87 (g/l) Number of SOL molecules: 3907 Processing topology Removing line #929 'SOL 533' from topology file (topol.top) Then running grompp for the next step ( neutralization ) grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr But the error is: Fatal error: number of coordinates in coordinate file (system_solv.gro, 18259) does not match topology (topol.top, 18159) For more information and tips for troubleshooting, please check the GROMACS Would you pleas help me? Do I need to modify the .top file before running grompp? Well, something doesn't match, so yes. But at the same time, if you're properly maintained the topology thus far, then you shouldn't have to. A difference of 100 atoms suggests there are 2 extra DPPC molecules in the coordinate file relative to the topology. I have no idea how you would have produced such a mismatch though. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] grompp in KALP15-DPPC
The number of DPPC molecules were 126. I changed it to 128 in topol.top, then the grompp didn't give me any fatal error. I had changed the number of DPPC in top file in last step when the inflateGRO reporst that 2 DPPC were removed. Now, 128 DPPC is acceptable! What does it mean? Is it sensible? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, August 25, 2012 8:59 PM Subject: Re: [gmx-users] grompp in KALP15-DPPC On 8/25/12 12:26 PM, Shima Arasteh wrote: Hi, I am doing the simulation of KALP15 in DPPC following the Justin's tutorial. For the step of solvation I ran this command: # genbox -cp system.gro -cs spc216.gro -o system_solv.gro -p topol.top The output of this step is as here: Reading solute configuration frame t= 1.000 Containing 17503 atoms in 3800 residues Initialising van der waals distances... WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. Reading solvent configuration 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 4x4x4 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 13824 residues Calculating Overlap... box_margin = 0.315 Removed 10608 atoms that were outside the box Neighborsearching with a cut-off of 1.125 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 1.125 Coulomb: 1.125 LJ: 1.125 System total charge: 0.000 Grid: 18 x 18 x 18 cells Successfully made neighbourlist nri = 152829, nrj = 41861902 Checking Protein-Solvent overlap: tested 3204927 pairs, removed 30048 atoms. Checking Solvent-Solvent overlap: tested 17610 pairs, removed 60 atoms. Added 252 molecules Generated solvent containing 756 atoms in 252 residues Writing generated configuration to system_solv.gro Back Off! I just backed up system_solv.gro to ./#system_solv.gro.3# frame t= 1.000 Output configuration contains 18259 atoms in 4052 residues Volume : 272.811 (nm^3) Density : 947.87 (g/l) Number of SOL molecules: 3907 Processing topology Removing line #929 'SOL 533' from topology file (topol.top) Then running grompp for the next step ( neutralization ) grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr But the error is: Fatal error: number of coordinates in coordinate file (system_solv.gro, 18259) does not match topology (topol.top, 18159) For more information and tips for troubleshooting, please check the GROMACS Would you pleas help me? Do I need to modify the .top file before running grompp? Well, something doesn't match, so yes. But at the same time, if you're properly maintained the topology thus far, then you shouldn't have to. A difference of 100 atoms suggests there are 2 extra DPPC molecules in the coordinate file relative to the topology. I have no idea how you would have produced such a mismatch though. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] grompp in KALP15-DPPC
On 8/25/12 12:41 PM, Shima Arasteh wrote: The number of DPPC molecules were 126. I changed it to 128 in topol.top, then the grompp didn't give me any fatal error. I had changed the number of DPPC in top file in last step when the inflateGRO reporst that 2 DPPC were removed. Now, 128 DPPC is acceptable! What does it mean? Is it sensible? Not in the least. You should make one change to the [molecules] (when InflateGRO deletes lipids) and never manually adjust it again. You need to check your work, because I suspect you're using the wrong files (either topology or coordinates) because suddenly there's a mismatch that shouldn't be happening. You can always check what's in your coordinate file with grep to do counting, e.g.: grep -c P8 (name of your coordinate file) That will tell you the number of DPPC lipids. Likewise, you can count water molecules (another common source of error) with: grep -c OW (name of your coordinate file) If your coordinate file somehow has 128 DPPC again, then you're using the wrong file. Once deleted, they don't get added back. -Justin Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, August 25, 2012 8:59 PM Subject: Re: [gmx-users] grompp in KALP15-DPPC On 8/25/12 12:26 PM, Shima Arasteh wrote: Hi, I am doing the simulation of KALP15 in DPPC following the Justin's tutorial. For the step of solvation I ran this command: # genbox -cp system.gro -cs spc216.gro -o system_solv.gro -p topol.top The output of this step is as here: Reading solute configuration frame t= 1.000 Containing 17503 atoms in 3800 residues Initialising van der waals distances... WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. Reading solvent configuration 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 4x4x4 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 13824 residues Calculating Overlap... box_margin = 0.315 Removed 10608 atoms that were outside the box Neighborsearching with a cut-off of 1.125 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 1.125 Coulomb: 1.125 LJ: 1.125 System total charge: 0.000 Grid: 18 x 18 x 18 cells Successfully made neighbourlist nri = 152829, nrj = 41861902 Checking Protein-Solvent overlap: tested 3204927 pairs, removed 30048 atoms. Checking Solvent-Solvent overlap: tested 17610 pairs, removed 60 atoms. Added 252 molecules Generated solvent containing 756 atoms in 252 residues Writing generated configuration to system_solv.gro Back Off! I just backed up system_solv.gro to ./#system_solv.gro.3# frame t= 1.000 Output configuration contains 18259 atoms in 4052 residues Volume : 272.811 (nm^3) Density: 947.87 (g/l) Number of SOL molecules: 3907 Processing topology Removing line #929 'SOL 533' from topology file (topol.top) Then running grompp for the next step ( neutralization ) grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr But the error is: Fatal error: number of coordinates in coordinate file (system_solv.gro, 18259) does not match topology (topol.top, 18159) For more information and tips for troubleshooting, please check the GROMACS Would you pleas help me? Do I need to modify the .top file before running grompp? Well, something doesn't match, so yes. But at the same time, if you're properly maintained the topology thus far, then you shouldn't have to. A difference of 100 atoms suggests there are 2 extra DPPC molecules in the coordinate file relative to the topology. I have no idea how you would have produced such a mismatch though. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] grompp in KALP15-DPPC
Thanks for your reply. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, August 25, 2012 9:16 PM Subject: Re: [gmx-users] grompp in KALP15-DPPC On 8/25/12 12:41 PM, Shima Arasteh wrote: The number of DPPC molecules were 126. I changed it to 128 in topol.top, then the grompp didn't give me any fatal error. I had changed the number of DPPC in top file in last step when the inflateGRO reporst that 2 DPPC were removed. Now, 128 DPPC is acceptable! What does it mean? Is it sensible? Not in the least. You should make one change to the [molecules] (when InflateGRO deletes lipids) and never manually adjust it again. You need to check your work, because I suspect you're using the wrong files (either topology or coordinates) because suddenly there's a mismatch that shouldn't be happening. You can always check what's in your coordinate file with grep to do counting, e.g.: grep -c P8 (name of your coordinate file) That will tell you the number of DPPC lipids. Likewise, you can count water molecules (another common source of error) with: grep -c OW (name of your coordinate file) If your coordinate file somehow has 128 DPPC again, then you're using the wrong file. Once deleted, they don't get added back. -Justin Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, August 25, 2012 8:59 PM Subject: Re: [gmx-users] grompp in KALP15-DPPC On 8/25/12 12:26 PM, Shima Arasteh wrote: Hi, I am doing the simulation of KALP15 in DPPC following the Justin's tutorial. For the step of solvation I ran this command: # genbox -cp system.gro -cs spc216.gro -o system_solv.gro -p topol.top The output of this step is as here: Reading solute configuration frame t= 1.000 Containing 17503 atoms in 3800 residues Initialising van der waals distances... WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. Reading solvent configuration 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 4x4x4 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 13824 residues Calculating Overlap... box_margin = 0.315 Removed 10608 atoms that were outside the box Neighborsearching with a cut-off of 1.125 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 1.125 Coulomb: 1.125 LJ: 1.125 System total charge: 0.000 Grid: 18 x 18 x 18 cells Successfully made neighbourlist nri = 152829, nrj = 41861902 Checking Protein-Solvent overlap: tested 3204927 pairs, removed 30048 atoms. Checking Solvent-Solvent overlap: tested 17610 pairs, removed 60 atoms. Added 252 molecules Generated solvent containing 756 atoms in 252 residues Writing generated configuration to system_solv.gro Back Off! I just backed up system_solv.gro to ./#system_solv.gro.3# frame t= 1.000 Output configuration contains 18259 atoms in 4052 residues Volume : 272.811 (nm^3) Density : 947.87 (g/l) Number of SOL molecules: 3907 Processing topology Removing line #929 'SOL 533' from topology file (topol.top) Then running grompp for the next step ( neutralization ) grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr But the error is: Fatal error: number of coordinates in coordinate file (system_solv.gro, 18259) does not match topology (topol.top, 18159) For more information and tips for troubleshooting, please check the GROMACS Would you pleas help me? Do I need to modify the .top file before running grompp? Well, something doesn't match, so yes. But at the same time, if you're properly maintained the topology thus far, then you shouldn't have to. A difference of 100 atoms suggests there are 2 extra DPPC molecules in the coordinate file relative to the topology. I have no idea how you would have produced such a mismatch though. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www
[gmx-users] how to optimize performance of IBM Power 775?
Beyond optimizing your number of cores and npme (by hand I guess in your case), you can try hyperthreading (talk to your sysadmins if you can not simply run 2N threads, where N is the number of cores. I found on a power 6 that if you have N cores, it is optimal to run 2N-1 threads, rather than 2N threads. Nevertheless, I have found that the IBM power 5 and power 6 machines run gromacs significantly slower than, for example, a Nehalem. I don't know if it's a lack of gromacs hardware-specific optimization or simply a function of the lower power consumption of the IBM power series. A number of years ago, I posted a few emails to this list on how to optimize compilation on the power machines (flags, etc). You should be able to find those by searching. Good luck, Chris. -- original message -- Our institute got a IBM Power 775 cluster and it claimed to be very good. However, it doesn't support g_tune_pme. I use the following script for job submission: #@ job_name = gromacs_job #@ output = gromacs.out #@ error = gromacs.err #@ class = kdm #@ node = 4 #@ tasks_per_node = 32 #@ wall_clock_limit = 01:00:00 #@ network.MPI = sn_all,not_shared,US,HIGH #@ notification = never #@ environment = COPY_ALL #@ job_type = parallel #@ queue mpiexec -n 128 /opt/gromacs/4.5.5/bin/mdrun -nosum -dlb yes -v -s md.tpr it is only 7 ns/day. However, in another cluster with the same system, Core number and parameters, I can get up to 30 ns/day. Does anybody have any advices for this issue? thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
