[gmx-users] Reg: MDS of docked comples
Hi there ... i am new to GROMACS ... however i am able to do mds of simple protein structures under default configurations ... now i want to simulate docked complexes .. the docking is done using autodock in order to see the hydrogen bond variations between the ligand and the active site lining residues but for this i don't have any protocol ... therefore if anyone can suggest me a standard protocol for simulating docked compexes along with the mdp files ... then please do suggest ... Regards Rohit -- Rohit Farmer M.Tech Bioinformatics Department of Computational Biology and Bioinformatics Jacob School of Biengineering and Biotechnology Sam Higginbottom Institute of Agriculture, Technology and Sciences (Formerly known as Allahabad Agricultural Institute - Deemed University) Allahabad, UP, INDIA - 211 007 Ph. No. 9839845093, 9415261403 e-Mail rohit.far...@gmail.com Blog http://rohitsspace.blogspot.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] Reg: MDS of docked comples
I recall that somewhere on the Gromacs website is the Drug-Enzyme tutorial by Kerrigan. That is what you are looking for. Andreas -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Rohit Farmer Sent: 16 February 2010 08:33 To: gmx-users@gromacs.org Subject: [gmx-users] Reg: MDS of docked comples Hi there ... i am new to GROMACS ... however i am able to do mds of simple protein structures under default configurations ... now i want to simulate docked complexes .. the docking is done using autodock in order to see the hydrogen bond variations between the ligand and the active site lining residues but for this i don't have any protocol ... therefore if anyone can suggest me a standard protocol for simulating docked compexes along with the mdp files ... then please do suggest ... Regards Rohit -- Rohit Farmer M.Tech Bioinformatics Department of Computational Biology and Bioinformatics Jacob School of Biengineering and Biotechnology Sam Higginbottom Institute of Agriculture, Technology and Sciences (Formerly known as Allahabad Agricultural Institute - Deemed University) Allahabad, UP, INDIA - 211 007 Ph. No. 9839845093, 9415261403 e-Mail rohit.far...@gmail.com Blog http://rohitsspace.blogspot.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Analysis of a simulation
On Tue, Feb 16, 2010 at 11:12 AM, sukesh chandra gain suk...@atc.tcs.comwrote: Dear All, It is not clear from manual how to analyse my requirements after simulation. Could you please help me in the following regards: Please have a look at the g_ tools. http://www.gromacs.org/Documentation/Gromacs_Utilities make a proper index file according to your needs using make_ndx or you can do it manually also. Have a look at Gromacs manual. Chapter 8. 1 How to get the graph on occupancy of hydrogen bond interactions of ligands throughout 5 ns simulation and occupancy of a particular salt-bridge throughout the simulation ? try g_hbond, g_saltbr depending on your system... you may look at other g_tools. 2 I want to get a graph of the distances of some particular co-factor atoms and active site residues atoms throughout the simulation. Suppose I want the distance graph between DPM:C9B and Arg7:CA for total simulation. g_dist 3 Average hydrogen bond distance between active site residues and ligand. g_hbond 4 RMSD of some particular residues from its initial structure. g_rms, g_rmsdist 5 Total formal charge residing at active site throughout the simulation (All +vely charge and -vely charge residues within 15 A radius of active site will be considered). g_saltbr after converting trajectory with trjorder. It would be a great help if you could kindly give some sample commands for these analysis. Sorry for lots of questions. Thank You. Regards, Sukesh -- Sukesh Chandra Gain TCS Innovation Labs Tata Consultancy Services Ltd. 'Deccan Park', Madhapur Hyderabad 500081 Phone: +91 40 6667 3572 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php Cheers, Saikat --- Saikat Banerjee Integrated Ph.D student Prof B. Bagchi's group Room no. 210 Solid State and Structural Chemistry Unit (SSCU) Indian Institute of Science Bangalore-560012 --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] md simulation of carbon nano tubes
Hi what is the best program and force field for md simulation of carbon nano tubes? Any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Poor load balancing
Carsten thank you for your response. I did same benchmark with 8 node and 16 node . But these experiments were done with PME instead of cutt-off. To optimize I changed cutt-of and fourier spacing. I wonder this results are acceptable and if need more optimization. Thanks. Deniz 8 node and cutt-of = 0.9 nm fourier_spacing=0.12 Average load imbalance: 4.0 % Part of the total run time spent waiting due to load imbalance: 1.4 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Average PME mesh/force load: 1.758 Part of the total run time spent waiting due to PP/PME imbalance: 15.7 % NOTE: 15.7 % performance was lost because the PME nodes had more work to do than the PP nodes. You might want to increase the number of PME nodes or increase the cut-off and the grid spacing. 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 Number G-CyclesSeconds % --- Domain decomp. 4 1001 36.253 15.5 1.4 Vsite constr. 4 50013.2371.4 0.1 Send X to PME 4 5001 10.3654.4 0.4 Comm. coord. 4 5001 15.1936.5 0.6 Neighbor search4 1001 279.944 120.010.8 Force 4 5001 451.185 193.517.4 Wait + Comm. F 4 5001 63.147 27.1 2.4 PME mesh 4 5001 940.073 403.136.3 Wait + Comm. X/F 4 5001 356.494 152.913.7 Wait + Recv. PME F 4 5001 345.820 148.313.3 Vsite spread 4 100026.5682.8 0.3 Write traj.4 10.3500.2 0.0 Update 4 5001 20.5258.8 0.8 Constraints4 5001 42.245 18.1 1.6 Comm. energies 4 50013.3771.4 0.1 Rest 4 18.3937.9 0.7 --- Total 82593.170 1112.0 100.0 --- Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time:139.000139.000100.0 2:19 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance:127.854 9.458 12.434 1.930 Finished mdrun on node 0 Mon Feb 15 17:34:48 2010 8 node cut-off = 1.0 nm and fourier_spacing=0.13 Average load imbalance: 3.4 % Part of the total run time spent waiting due to load imbalance: 1.7 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Average PME mesh/force load: 1.129 Part of the total run time spent waiting due to PP/PME imbalance: 3.7 % 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 Number G-CyclesSeconds % --- Domain decomp. 4 1001 35.777 15.3 1.5 Vsite constr. 4 50012.6201.1 0.1 Send X to PME 4 5001 10.1824.4 0.4 Comm. coord. 4 5001 15.7276.7 0.7 Neighbor search4 1001 275.561 117.911.8 Force 4 5001 576.720 246.724.7 Wait + Comm. F 4 5001 69.631 29.8 3.0 PME mesh 4 5001 752.485 321.832.2 Wait + Comm. X/F 4 5001 416.550 178.217.8 Wait + Recv. PME F 4 5001 91.857 39.3 3.9 Vsite spread 4 100026.4562.8 0.3 Write traj.4 10.4260.2 0.0 Update 4 5001 20.5778.8 0.9 Constraints4 5001 41.959 17.9 1.8 Comm. energies 4 50012.9671.3 0.1 Rest 4 18.6128.0 0.8 --- Total 82338.108 1000.0 100.0 --- Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time:125.000125.000100.0 2:05 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance:190.198 11.789 13.827 1.736 Finished mdrun on node 0 Mon Feb 15 22:10:46 2010
Re: [gmx-users] md simulation of carbon nano tubes
leila karami wrote: Hi what is the best program and force field for md simulation of carbon nano tubes? Any help will highly appreciated! Search the literature. There are numerous reports of CNT simulations, many of them conducted with Gromacs. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] undesired aggregation
Hi. I was trying to simulate the behaviour of N-isopropyl propionamide, CH3-CH2-CO-NH-CH-(CH3)2 (NIPPA) in aqueous solution. This molecule has an inverted solubility behaviour with temperature and it displays a miscibility gap in water for temperatures higher than about 30°C. Experiments show that at 293 K and 1 atm the water/NIPPA omogeneous solution phase is stable at any composition. I performed a few NPT MD simulations of NIPPA in water SPC using the 45A3 force field, at different NIPPA concentrations, 293 K (Nose Hoover) and 1 atm (Parrinello Rahman), PME for electrostatic. Two typical systems contained [288 NIPPA molecules and 1680 water molecules] or [166 NIPPA and 4140 water molecules]. In the starting configuration the NIPPA molecules were randomly placed and solvated. I was very surprised to see that after 2 ns ( time step 2 fs) the NIPPA molecules aggregated, in several ways (layer, cylindrical tube, spherical object) depending on the NIPPA concentration, whereas I was expecting a complete solubility in water. In a further run at 273 K ( a temperature about 30 degrees lower than the critical temperature) I found the same aggregation effect. What do you think? Am I beyond the possibilties of the simulation? Any comment is welcome. Thanks in advance Ester P.S. I found in the literature that the DPPC self-assembly was modeled in MD simulations ( de Vries et al JACS 2004) at 323 K, a temperature higher than the transition temperature of DPPC. Why did the Authors use a T where the organized phase is unstable? I was wondering since also for my system the temperature is a crucial parameter. Ester Chiessi Dipartimento di Scienze e Tecnologie Chimiche Università di Roma Tor Vergata Via della Ricerca Scientifica 00133 Roma http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm tel: *39*6*72594462-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Average structure -s
Hi everyone, please I need to calculate RMSF after fitting to the average structure of my MD simulation. Can anyone tell me how to do that? (especially, how to calculate the average structure) Another question that may sound stupid: does the -s have the same function with trjconv g_rmsf? Can anyone clarify this option for me? Thank you Carla -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] undesired aggregation
Hi, This subject is extremely sensitive to force field and simulation accuracy. The small forces driving aggregation are the result of many, large counteracting forces. Force fields often give the right behavior, but nearly never at the correct temperature unless they have been explicitly parametrized for this. I would not expect the Gromos force field to behave too badly though, since it has been parametrized to reproduce partitioning between water and cyclohexane. What are your cut-off's and electrostatics settings? Berk From: ester.chie...@uniroma2.it To: gmx-users@gromacs.org Date: Tue, 16 Feb 2010 14:35:11 +0100 Subject: [gmx-users] undesired aggregation Hi. I was trying to simulate the behaviour of N-isopropyl propionamide, CH3-CH2-CO-NH-CH-(CH3)2 (NIPPA) in aqueous solution. This molecule has an inverted solubility behaviour with temperature and it displays a miscibility gap in water for temperatures higher than about 30°C. Experiments show that at 293 K and 1 atm the water/NIPPA omogeneous solution phase is stable at any composition. I performed a few NPT MD simulations of NIPPA in water SPC using the 45A3 force field, at different NIPPA concentrations, 293 K (Nose Hoover) and 1 atm (Parrinello Rahman), PME for electrostatic. Two typical systems contained [288 NIPPA molecules and 1680 water molecules] or [166 NIPPA and 4140 water molecules]. In the starting configuration the NIPPA molecules were randomly placed and solvated. I was very surprised to see that after 2 ns ( time step 2 fs) the NIPPA molecules aggregated, in several ways (layer, cylindrical tube, spherical object) depending on the NIPPA concentration, whereas I was expecting a complete solubility in water. In a further run at 273 K ( a temperature about 30 degrees lower than the critical temperature) I found the same aggregation effect. What do you think? Am I beyond the possibilties of the simulation? Any comment is welcome. Thanks in advance Ester P.S. I found in the literature that the DPPC self-assembly was modeled in MD simulations ( de Vries et al JACS 2004) at 323 K, a temperature higher than the transition temperature of DPPC. Why did the Authors use a T where the organized phase is unstable? I was wondering since also for my system the temperature is a crucial parameter. Ester Chiessi Dipartimento di Scienze e Tecnologie Chimiche Università di Roma Tor Vergata Via della Ricerca Scientifica 00133 Roma http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm tel: *39*6*72594462 _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 70, Issue 92
Hi what is the best program and force field for md simulation of carbon nano tubes? There's no such one as for me. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Average structure -s
On 17/02/10 01:12, Carla Jamous wrote: Hi everyone, please I need to calculate RMSF after fitting to the average structure of my MD simulation. Can anyone tell me how to do that? (especially, how to calculate the average structure) g_rmsf. There's a section in the manual that gives a breakdown of the GROMACS tools by topic that can help guide you. Another question that may sound stupid: does the -s have the same function with trjconv g_rmsf? Can anyone clarify this option for me? Use the -h flag to the tool to see a description of how things work. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] pbc whole
Hi Justin, Thank you for your answer but I'm still not getting my ligand to stay in the box. I tried the following(after taking a look at the mailing list archive): trjconv -s a.tpr -f b.xtc -o c.xtc -center -ur compact -pbc mol (centering on Protein) trjconv -s d.tpr -f c.xtc -o f.xtc -fit rot+trans So please do you have another advise to give me? Thanks Carla On Mon, Feb 15, 2010 at 4:32 PM, Justin A. Lemkul jalem...@vt.edu wrote: Carla Jamous wrote: Hi everyone, I'm using this command to extract my protein and my ligand from the trajectory. trjconv -f prot_md60ns.xtc -s prot_md50.tpr -fit rot+trans -pbc whole -n prot_wat.ndx -o prot_ligand_60ns.xtc grps outtrj Before, I had a problem with residues of my protein showing at the other end of the box, when I display my .xtc with VMD. the -pbc whole fixed it. However, now I have another issue: my ligand is at the other end of the box. So please can anyone tell me what can I do to fix that and get a reasonable RMSD value? You may need several more iterations of trjconv (one rarely does the trick), employing -pbc nojump, -pbc cluster, and/or -center. For protein-ligand complexes, I have often found that the combination of: trjconv -pbc mol -ur compact -center (centering on Protein) does the trick. And it makes molecules whole, as well :) I think there are also some breakdowns (documented somewhere in the list archive) when applying -fit and -pbc in the same step. I believe it is recommended to fix PBC first, then applying any sort of fitting in a separate, subsequent step. -Justin Thank you Carla -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Average structure -s
I looked at g_rmsf -h but the problem is that it's not clear enough. The help doesn't state how g_rmsf works what does it calculate exactly. Because the definition of an RMSF is the following: the mean-square fluctuation is a measure of the deviation between the position of particle i and some reference position. Typically, this reference position will be the time-averaged position of the same particle i. So does g_rmsf calculate the average structure then the RMSF according to this average structure? Or does it calculate the RMSF after fitting to a reference structure that I would have specified with the option -s? Thanks Carla On Tue, Feb 16, 2010 at 3:54 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 17/02/10 01:12, Carla Jamous wrote: Hi everyone, please I need to calculate RMSF after fitting to the average structure of my MD simulation. Can anyone tell me how to do that? (especially, how to calculate the average structure) g_rmsf. There's a section in the manual that gives a breakdown of the GROMACS tools by topic that can help guide you. Another question that may sound stupid: does the -s have the same function with trjconv g_rmsf? Can anyone clarify this option for me? Use the -h flag to the tool to see a description of how things work. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] restarting mdrun
Hello gmxusers !!! I want to continue my simulation, from where the point where it stopped. The gmxcheck on .trr and cpt files are as: $gmxcheck -f state.cpt Checking file state.cpt # Atoms 186864 Last frame -1 time 9362.500 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 $gmxcheck -f 5-10.trr Checking file 5-10.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 5169.500 # Atoms 186864 Reading frame8000 time 9169.500 Item#frames Timestep (ps) Step 83950.5 Time 83950.5 Lambda83950.5 Coords83950.5 Velocities83950.5 Forces 0 Box 83950.5 There is a mismatch of time in both the outputs. The date of modification of both the files as shown are: Feb 15 19:55 state.cpt $date -r 5-10.trr Mon Feb 15 19:59:56 IST 2010 The cpt file shows time greater than the trr file. But the time of modification of cpt file is less than trr file. Cannot understand the, how to restart the mdrun. And the size of the trr file is 36GB. Can I use the append flag in mdrun for gmx 4.0.5. Kindly suggest. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Poor load balancing
Deniz, for calculations with PME you might want to use the g_tune_pme tools that helps to find the optimal settings on a given number of cores. For Gromacs 4.0.x you can download it from http://www.mpibpc.mpg.de/home/grubmueller/projects/MethodAdvancements/Gromacs/ You find installation instructions on the top of the g_tune_pme.c file. Carsten On Feb 16, 2010, at 1:41 PM, Deniz KARASU wrote: Carsten thank you for your response. I did same benchmark with 8 node and 16 node . But these experiments were done with PME instead of cutt-off. To optimize I changed cutt-of and fourier spacing. I wonder this results are acceptable and if need more optimization. Thanks. Deniz 8 node and cutt-of = 0.9 nm fourier_spacing=0.12 Average load imbalance: 4.0 % Part of the total run time spent waiting due to load imbalance: 1.4 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Average PME mesh/force load: 1.758 Part of the total run time spent waiting due to PP/PME imbalance: 15.7 % NOTE: 15.7 % performance was lost because the PME nodes had more work to do than the PP nodes. You might want to increase the number of PME nodes or increase the cut-off and the grid spacing. 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 Number G-CyclesSeconds % --- Domain decomp. 4 1001 36.253 15.5 1.4 Vsite constr. 4 50013.2371.4 0.1 Send X to PME 4 5001 10.3654.4 0.4 Comm. coord. 4 5001 15.1936.5 0.6 Neighbor search4 1001 279.944 120.010.8 Force 4 5001 451.185 193.517.4 Wait + Comm. F 4 5001 63.147 27.1 2.4 PME mesh 4 5001 940.073 403.136.3 Wait + Comm. X/F 4 5001 356.494 152.913.7 Wait + Recv. PME F 4 5001 345.820 148.313.3 Vsite spread 4 100026.5682.8 0.3 Write traj.4 10.3500.2 0.0 Update 4 5001 20.5258.8 0.8 Constraints4 5001 42.245 18.1 1.6 Comm. energies 4 50013.3771.4 0.1 Rest 4 18.3937.9 0.7 --- Total 82593.170 1112.0 100.0 --- Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time:139.000139.000100.0 2:19 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance:127.854 9.458 12.434 1.930 Finished mdrun on node 0 Mon Feb 15 17:34:48 2010 8 node cut-off = 1.0 nm and fourier_spacing=0.13 Average load imbalance: 3.4 % Part of the total run time spent waiting due to load imbalance: 1.7 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Average PME mesh/force load: 1.129 Part of the total run time spent waiting due to PP/PME imbalance: 3.7 % 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 Number G-CyclesSeconds % --- Domain decomp. 4 1001 35.777 15.3 1.5 Vsite constr. 4 50012.6201.1 0.1 Send X to PME 4 5001 10.1824.4 0.4 Comm. coord. 4 5001 15.7276.7 0.7 Neighbor search4 1001 275.561 117.911.8 Force 4 5001 576.720 246.724.7 Wait + Comm. F 4 5001 69.631 29.8 3.0 PME mesh 4 5001 752.485 321.832.2 Wait + Comm. X/F 4 5001 416.550 178.217.8 Wait + Recv. PME F 4 5001 91.857 39.3 3.9 Vsite spread 4 100026.4562.8 0.3 Write traj.4 10.4260.2 0.0 Update 4 5001 20.5778.8 0.9 Constraints4 5001 41.959 17.9 1.8 Comm. energies 4 50012.9671.3 0.1 Rest 4 18.6128.0 0.8
Re: [gmx-users] Average structure -s
On 17/02/10 02:38, Carla Jamous wrote: I looked at g_rmsf -h but the problem is that it's not clear enough. The help doesn't state how g_rmsf works what does it calculate exactly. Because the definition of an RMSF is the following: the mean-square fluctuation is a measure of the deviation between the position of particle i and some reference position. Typically, this reference position will be the time-averaged position of the same particle i. So does g_rmsf calculate the average structure then the RMSF according to this average structure? From g_rmsf -h: g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions after (optionally) fitting to a reference frame. So it will do what you want. Apparently the fitting is optional. Further down you can see that the -s file is not optional, so presumably the program will prompt you about whether or not you want fitting to the -s structure. Try it and see. Or does it calculate the RMSF after fitting to a reference structure that I would have specified with the option -s? The usual procedure is to read the documentation and then experiment. Software documentation is never exhaustive if the toolset is powerful - otherwise, it would grow exponentially unwieldy as the number of different user choices grows. A few minutes' thought will suggest ways you can test to see if any fitting is occurring. Mark On Tue, Feb 16, 2010 at 3:54 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 17/02/10 01:12, Carla Jamous wrote: Hi everyone, please I need to calculate RMSF after fitting to the average structure of my MD simulation. Can anyone tell me how to do that? (especially, how to calculate the average structure) g_rmsf. There's a section in the manual that gives a breakdown of the GROMACS tools by topic that can help guide you. Another question that may sound stupid: does the -s have the same function with trjconv g_rmsf? Can anyone clarify this option for me? Use the -h flag to the tool to see a description of how things work. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Power6 @ 4.7 Ghz vs Xeon E5472 @ 3.00GHz
Dear Gromacs users, I have been installing Gromacs on a Power6 4.7 GHz with Infiniband, GBit-Ethernet before calling configure, I set: export LDFLAGS=-L/gpfs/schraven/fftw3/lib export CPPFLAGS=-I/gpfs/schraven/fftw3/include export CC=mpcc_r -q64 export CFLAGS=-O3 -qstrict -qarch=auto -qtune=auto export CXX=mpCC_r -q64 export CXXFLAGS=-O3 -qstrict -qarch=auto -qtune=auto export F77=mpxlf_r -q64 ### O3 gives warning: The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. export FFLAGS=-O3 -qstrict -qnoprefetch -qarch=auto -qtune=auto export LIBS=-lmass export FLIBS= -xlf -xlf90 export OBJECT_MODE=64 I run on both machines at 8 cores (so within the board), and find the 8 power6 cores to be 4-5 times slower (!) than the 8 intel xeon cores. Does anyone have similar experience between these machines? Are there some things I should check? It's a bit useless to use the power6 at all with these kind of speeds, but they were already here anyway and amazon's 30 day refund on retour has expired already ;) Hopefully I'm doing something wrong and the situation can still be improved? Greetings, Pim -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] restarting mdrun
On 17/02/10 02:52, Chandan Choudhury wrote: Hello gmxusers !!! I want to continue my simulation, from where the point where it stopped. The gmxcheck on .trr and cpt files are as: $gmxcheck -f state.cpt Checking file state.cpt # Atoms 186864 Last frame -1 time 9362.500 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 $gmxcheck -f 5-10.trr Checking file 5-10.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 5169.500 # Atoms 186864 Reading frame8000 time 9169.500 Item#frames Timestep (ps) Step 83950.5 Time 83950.5 Lambda83950.5 Coords83950.5 Velocities83950.5 Forces 0 Box 83950.5 There is a mismatch of time in both the outputs. The date of modification of both the files as shown are: Feb 15 19:55 state.cpt $date -r 5-10.trr Mon Feb 15 19:59:56 IST 2010 The cpt file shows time greater than the trr file. But the time of modification of cpt file is less than trr file. If the simulation stopped catastrophically, then the timestamp could easily differ, especially if the .cpt is opened, written to and closed periodically, and the .trr is open continuously. Cannot understand the, how to restart the mdrun. And the size of the trr file is 36GB. Can I use the append flag in mdrun for gmx 4.0.5. Search the webpage for suggestions. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Power6 @ 4.7 Ghz vs Xeon E5472 @ 3.00GHz
On 17/02/10 03:06, pim schravendijk wrote: Dear Gromacs users, I have been installing Gromacs on a Power6 4.7 GHz with Infiniband, GBit-Ethernet before calling configure, I set: export LDFLAGS=-L/gpfs/schraven/fftw3/lib export CPPFLAGS=-I/gpfs/schraven/fftw3/include export CC=mpcc_r -q64 export CFLAGS=-O3 -qstrict -qarch=auto -qtune=auto export CXX=mpCC_r -q64 export CXXFLAGS=-O3 -qstrict -qarch=auto -qtune=auto export F77=mpxlf_r -q64 ### O3 gives warning: The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. export FFLAGS=-O3 -qstrict -qnoprefetch -qarch=auto -qtune=auto export LIBS=-lmass export FLIBS= -xlf -xlf90 export OBJECT_MODE=64 I run on both machines at 8 cores (so within the board), and find the 8 power6 cores to be 4-5 times slower (!) than the 8 intel xeon cores. Does anyone have similar experience between these machines? Are there some things I should check? It's a bit useless to use the power6 at all with these kind of speeds, but they were already here anyway and amazon's 30 day refund on retour has expired already ;) Hopefully I'm doing something wrong and the situation can still be improved? This issue might have been discussed on the list before, have a search. I suspect the issue is that there are no optimized inner loops for Power6 as there are for x86. You can see what GROMACS is finding and doing in the configure output. Probably GROMACS is finding nothing useful and falling back on generic C versions of such loops. You should experiment with --enable-fortran to try the generic FORTRAN versions. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] pbc whole
Carla Jamous wrote: Hi Justin, Thank you for your answer but I'm still not getting my ligand to stay in the box. I tried the following(after taking a look at the mailing list archive): trjconv -s a.tpr -f b.xtc -o c.xtc -center -ur compact -pbc mol (centering on Protein) trjconv -s d.tpr -f c.xtc -o f.xtc -fit rot+trans So please do you have another advise to give me? If that's not working, then I wonder if your ligand is still actually bound to your protein :) The above sequence always works for me, as long as there actually is a complex. You can also try -pbc cluster, but I know that algorithm can hang. -Justin Thanks Carla On Mon, Feb 15, 2010 at 4:32 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Carla Jamous wrote: Hi everyone, I'm using this command to extract my protein and my ligand from the trajectory. trjconv -f prot_md60ns.xtc -s prot_md50.tpr -fit rot+trans -pbc whole -n prot_wat.ndx -o prot_ligand_60ns.xtc grps outtrj Before, I had a problem with residues of my protein showing at the other end of the box, when I display my .xtc with VMD. the -pbc whole fixed it. However, now I have another issue: my ligand is at the other end of the box. So please can anyone tell me what can I do to fix that and get a reasonable RMSD value? You may need several more iterations of trjconv (one rarely does the trick), employing -pbc nojump, -pbc cluster, and/or -center. For protein-ligand complexes, I have often found that the combination of: trjconv -pbc mol -ur compact -center (centering on Protein) does the trick. And it makes molecules whole, as well :) I think there are also some breakdowns (documented somewhere in the list archive) when applying -fit and -pbc in the same step. I believe it is recommended to fix PBC first, then applying any sort of fitting in a separate, subsequent step. -Justin Thank you Carla -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] restarting mdrun
Hi Mark !!! Thanks for answering. My query is how do I restart my mdrun because the command nohup mpirun -np 16 -machinefile mac mdrun -s md5-10.tpr -cpi state.cpt -append will not start from where the trajectory was stopped (i.e; time 9169.500). As this command will continue the simulation from where the cpt file was written. Any suggestions?? chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Feb 16, 2010 at 9:36 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 17/02/10 02:52, Chandan Choudhury wrote: Hello gmxusers !!! I want to continue my simulation, from where the point where it stopped. The gmxcheck on .trr and cpt files are as: $gmxcheck -f state.cpt Checking file state.cpt # Atoms 186864 Last frame -1 time 9362.500 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 $gmxcheck -f 5-10.trr Checking file 5-10.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 5169.500 # Atoms 186864 Reading frame8000 time 9169.500 Item#frames Timestep (ps) Step 83950.5 Time 83950.5 Lambda83950.5 Coords83950.5 Velocities83950.5 Forces 0 Box 83950.5 There is a mismatch of time in both the outputs. The date of modification of both the files as shown are: Feb 15 19:55 state.cpt $date -r 5-10.trr Mon Feb 15 19:59:56 IST 2010 The cpt file shows time greater than the trr file. But the time of modification of cpt file is less than trr file. If the simulation stopped catastrophically, then the timestamp could easily differ, especially if the .cpt is opened, written to and closed periodically, and the .trr is open continuously. Cannot understand the, how to restart the mdrun. And the size of the trr file is 36GB. Can I use the append flag in mdrun for gmx 4.0.5. Search the webpage for suggestions. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] restarting mdrun
Chandan Choudhury wrote: Hi Mark !!! Thanks for answering. My query is how do I restart my mdrun because the command nohup mpirun -np 16 -machinefile mac mdrun -s md5-10.tpr -cpi state.cpt -append will not start from where the trajectory was stopped (i.e; time 9169.500). As this command will continue the simulation from where the cpt file was written. Right, it will start from whenever the checkpoint was written. You should also have a state_prev.cpt that is a backup in case this type of thing happens; it may help. Regardless, with a 36-GB .trr file, the -append option will not work. Leave it out and use trjcat later. -Justin Any suggestions?? chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Feb 16, 2010 at 9:36 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 17/02/10 02:52, Chandan Choudhury wrote: Hello gmxusers !!! I want to continue my simulation, from where the point where it stopped. The gmxcheck on .trr and cpt files are as: $gmxcheck -f state.cpt Checking file state.cpt # Atoms 186864 Last frame -1 time 9362.500 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 $gmxcheck -f 5-10.trr Checking file 5-10.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 5169.500 # Atoms 186864 Reading frame8000 time 9169.500 Item#frames Timestep (ps) Step 83950.5 Time 83950.5 Lambda83950.5 Coords83950.5 Velocities83950.5 Forces 0 Box 83950.5 There is a mismatch of time in both the outputs. The date of modification of both the files as shown are: Feb 15 19:55 state.cpt $date -r 5-10.trr Mon Feb 15 19:59:56 IST 2010 The cpt file shows time greater than the trr file. But the time of modification of cpt file is less than trr file. If the simulation stopped catastrophically, then the timestamp could easily differ, especially if the .cpt is opened, written to and closed periodically, and the .trr is open continuously. Cannot understand the, how to restart the mdrun. And the size of the trr file is 36GB. Can I use the append flag in mdrun for gmx 4.0.5. Search the webpage for suggestions. Mark -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] restarting mdrun
Thanks Justin !! But my state_prev.cpt file shows $gmxcheck -f state_prev.cpt Checking file state_prev.cpt # Atoms 186864 Last frame -1 time 9346.700 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 Here also the time is greater than the .trr file. Cant understand how to overcome it. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Feb 16, 2010 at 11:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: Chandan Choudhury wrote: Hi Mark !!! Thanks for answering. My query is how do I restart my mdrun because the command nohup mpirun -np 16 -machinefile mac mdrun -s md5-10.tpr -cpi state.cpt -append will not start from where the trajectory was stopped (i.e; time 9169.500). As this command will continue the simulation from where the cpt file was written. Right, it will start from whenever the checkpoint was written. You should also have a state_prev.cpt that is a backup in case this type of thing happens; it may help. Regardless, with a 36-GB .trr file, the -append option will not work. Leave it out and use trjcat later. -Justin Any suggestions?? chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Feb 16, 2010 at 9:36 PM, Mark Abraham mark.abra...@anu.edu.aumailto: mark.abra...@anu.edu.au wrote: On 17/02/10 02:52, Chandan Choudhury wrote: Hello gmxusers !!! I want to continue my simulation, from where the point where it stopped. The gmxcheck on .trr and cpt files are as: $gmxcheck -f state.cpt Checking file state.cpt # Atoms 186864 Last frame -1 time 9362.500 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 $gmxcheck -f 5-10.trr Checking file 5-10.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 5169.500 # Atoms 186864 Reading frame8000 time 9169.500 Item#frames Timestep (ps) Step 83950.5 Time 83950.5 Lambda83950.5 Coords83950.5 Velocities83950.5 Forces 0 Box 83950.5 There is a mismatch of time in both the outputs. The date of modification of both the files as shown are: Feb 15 19:55 state.cpt $date -r 5-10.trr Mon Feb 15 19:59:56 IST 2010 The cpt file shows time greater than the trr file. But the time of modification of cpt file is less than trr file. If the simulation stopped catastrophically, then the timestamp could easily differ, especially if the .cpt is opened, written to and closed periodically, and the .trr is open continuously. Cannot understand the, how to restart the mdrun. And the size of the trr file is 36GB. Can I use the append flag in mdrun for gmx 4.0.5. Search the webpage for suggestions. Mark --gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] restarting mdrun
On 17/02/10 04:43, Chandan Choudhury wrote: Thanks Justin !! But my state_prev.cpt file shows $gmxcheck -f state_prev.cpt Checking file state_prev.cpt # Atoms 186864 Last frame -1 time 9346.700 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 Here also the time is greater than the .trr file. Cant understand how to overcome it. Your checkpoint interval need not match your .trr-writing interval - see your .mdp file. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Restarting mdrun
Hi Chadan, I have used the two commands below to CONTINUE a run and they worked fine for me. I am also using gromacs-4.0.5. tpbconv -s wfullmdrun_extend2.tpr -extend 2000 -o wfullmdrun_extend3.tpr mdrun -s wfullmdrun_extend3.tpr -o wfullmdrun_traj.trr -e wfullmdrun_ener.edr -g md.log -cpi state_prev.cpt -append The first command includes the amount of time by which you want to extend your run. The second one just appends the results to your existing files. In this second command, you are using the new .tpr file you created in the first command. Use the state.cpt file instead of the state_prev.cpt file in order to avoid losing time. Hope this helps. Lum On 17/02/10 02:52, Chandan Choudhury wrote: Hello gmxusers !!! I want to continue my simulation, from where the point where it stopped. The gmxcheck on .trr and cpt files are as: $gmxcheck -f state.cpt Checking file state.cpt # Atoms 186864 Last frame -1 time 9362.500 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 $gmxcheck -f 5-10.trr Checking file 5-10.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 5169.500 # Atoms 186864 Reading frame8000 time 9169.500 Item#frames Timestep (ps) Step 83950.5 Time 83950.5 Lambda83950.5 Coords83950.5 Velocities83950.5 Forces 0 Box 83950.5 There is a mismatch of time in both the outputs. The date of modification of both the files as shown are: Feb 15 19:55 state.cpt $date -r 5-10.trr Mon Feb 15 19:59:56 IST 2010 The cpt file shows time greater than the trr file. But the time of modification of cpt file is less than trr file. If the simulation stopped catastrophically, then the timestamp could easily differ, especially if the .cpt is opened, written to and closed periodically, and the .trr is open continuously. Cannot understand the, how to restart the mdrun. And the size of the trr file is 36GB. Can I use the append flag in mdrun for gmx 4.0.5. Search the webpage for suggestions. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] restarting mdrun
Below is my .mdp file. The timestep dt shows as 0.001 ps title= protein cpp = /lib/cpp ; RUN CONTROL integrator = md nsteps = 300 dt = 0.001 ; NEIGHBOR SEARCHING nstlist = 10 ns_type = grid pbc = xyz rlist= 0.9 ; OUTPUT CONTROL nstxout = 500 nstvout = 500 nstxtcout= 0 nstlog = 10 constraints = all-bonds nstenergy= 100 ; OPTION FOR ELECTROSTATIC AND VDW coulombtype = PME rcoulomb_switch = 0 rcoulomb = 0.9 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon_r= 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw_switch = 0 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Extension of the potential lookup tables beyond the cut-off table-extension = 2.5 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.28 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS tcoupl = V-rescale tc_grps = SOL Protein Na tau_t= 0.1 0.1 0.1 ref_t= 300 300 300 Pcoupl = Berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 gen_vel = yes gen_temp = 300 -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Feb 16, 2010 at 11:27 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 17/02/10 04:43, Chandan Choudhury wrote: Thanks Justin !! But my state_prev.cpt file shows $gmxcheck -f state_prev.cpt Checking file state_prev.cpt # Atoms 186864 Last frame -1 time 9346.700 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 Here also the time is greater than the .trr file. Cant understand how to overcome it. Your checkpoint interval need not match your .trr-writing interval - see your .mdp file. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Restarting mdrun
Thanks Lum !!! I had already used the suggestion you mentioned. But my problem is somewhat different. You can go through my previous mail, for more information. Thanks. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Feb 16, 2010 at 11:42 PM, Lum Nforbi lumngwe...@gmail.com wrote: Hi Chadan, I have used the two commands below to CONTINUE a run and they worked fine for me. I am also using gromacs-4.0.5. tpbconv -s wfullmdrun_extend2.tpr -extend 2000 -o wfullmdrun_extend3.tpr mdrun -s wfullmdrun_extend3.tpr -o wfullmdrun_traj.trr -e wfullmdrun_ener.edr -g md.log -cpi state_prev.cpt -append The first command includes the amount of time by which you want to extend your run. The second one just appends the results to your existing files. In this second command, you are using the new .tpr file you created in the first command. Use the state.cpt file instead of the state_prev.cpt file in order to avoid losing time. Hope this helps. Lum On 17/02/10 02:52, Chandan Choudhury wrote: Hello gmxusers !!! I want to continue my simulation, from where the point where it stopped. The gmxcheck on .trr and cpt files are as: $gmxcheck -f state.cpt Checking file state.cpt # Atoms 186864 Last frame -1 time 9362.500 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 $gmxcheck -f 5-10.trr Checking file 5-10.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 5169.500 # Atoms 186864 Reading frame8000 time 9169.500 Item#frames Timestep (ps) Step 83950.5 Time 83950.5 Lambda83950.5 Coords83950.5 Velocities83950.5 Forces 0 Box 83950.5 There is a mismatch of time in both the outputs. The date of modification of both the files as shown are: Feb 15 19:55 state.cpt $date -r 5-10.trr Mon Feb 15 19:59:56 IST 2010 The cpt file shows time greater than the trr file. But the time of modification of cpt file is less than trr file. If the simulation stopped catastrophically, then the timestamp could easily differ, especially if the .cpt is opened, written to and closed periodically, and the .trr is open continuously. Cannot understand the, how to restart the mdrun. And the size of the trr file is 36GB. Can I use the append flag in mdrun for gmx 4.0.5. Search the webpage for suggestions. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Is that true?
Hi, someone can told me if this affirmative is true for GROMACS 4.0? *The force fields and water models available for biomolecules have been developed for room temperature simulations* Or where I can find in the manual about this subject? Thanks, -- Mauricio UFRGS -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Is that true?
Maurício Menegatti Rigo wrote: Hi, someone can told me if this affirmative is true for GROMACS 4.0? /The force fields and water models available for biomolecules have been developed for room temperature simulations/ Or where I can find in the manual about this subject? I would suggest looking at the primary literature for the force fields and water models commonly used in biomolecular simulation. The Gromacs manual will not give these details. Most biomolecular force fields have been parameterized for condensed-phase simulations at a fairly narrow range of physiologically-relevant temperatures. Any extensions or modifications of these force fields should be documented in published papers. -Justin Thanks, -- Mauricio UFRGS -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] restarting mdrun
On 17/02/10 04:43, Chandan Choudhury wrote: Thanks Justin !! But my state_prev.cpt file shows $gmxcheck -f state_prev.cpt Checking file state_prev.cpt # Atoms 186864 Last frame -1 time 9346.700 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 Here also the time is greater than the .trr file. Cant understand how to overcome it. There's no reason any of this has to match. The checkpoint file is written according to the interval supplied with mdrun -cpt, default 15 minutes. The .trr file is written every so many steps per the .mdp flags. So their contents will generally not match at any point before the end of a run. They will match if it terminates normally. Simlarly the filesystem timestamp that gets recorded can vary with a whole pile of system variables, and need not match either. This is all fine. Under GROMACS 4.x, the purpose of the .cpt is to facilitate timely restarts without having to save excessive amounts of information in the trajectory file. Instead you can just focus on storing the data in your trajectory files that you need for your analysis. The website pages talk more about this. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
