[gmx-users] Low GPU utilization
Dear Gromacs users, I'm running a simulation between LASR receptor and Quercetin on Q6600, GTX 960, CPU utilization is about 90%, but GPU is only 25-30%(Nvidia X server tools).The system is only 28643 atoms and dt = 2 fs. This is the mdp settings: ; Run parametersdefine = -DPOSRES_B ; Lets seeintegrator = md ; leap-frog integratornsteps = 500 ; 2 * 50 = 1000 ps (1 ns)dt = 0.002 ; 2 fs; Output controlnstxout = 0 ; suppress .trr output nstvout = 0 ; suppress .trr outputnstenergy = 1000 ; save energies every 2 psnstlog = 1000 ; update log file every 2 psnstxout-compressed = 1000 ; write .xtc trajectory every 2 pscompressed-x-grps = Systemenergygrps = Protein HSL; Bond parameterscontinuation = yes ; first dynamics runconstraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrainedlincs_iter = 1 ; accuracy of LINCSlincs_order = 4 ; also related to accuracy; Neighborsearchingcutoff-scheme = Verletns_type = grid ; search neighboring grid cellsnstlist = 10 ; 20 fsrcoulomb = 1.4rvdw = 1.4 ; short-range van der Waals cutoff (in nm); Electrostaticscoulombtype = PME ; Particle Mesh Ewald for long-range electrostaticspme_order = 4 ; cubic interpolationfourierspacing = 0.16 ; grid spacing for FFT; Temperature coupling is ontcoupl = V-rescale ; modified Berendsen thermostattc-grps = Protein_HSL Water_and_ions ; two coupling groups - more accuratetau_t = 0.1 0.1 ; time constant, in psref_t = 300 300 ; reference temperature, one for each group, in K; Pressure coupling is offpcoupl = Parrinello-Rahman ; pressure coupling is on for NPTpcoupltype = isotropic ; uniform scaling of box vectorstau_p = 2.0 ; time constant, in psref_p = 1.0 ; reference pressure, in barcompressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1; Periodic boundary conditionspbc = xyz ; 3-D PBC; Dispersion correctionDispCorr = EnerPres ; account for cut-off vdW scheme; Velocity generationgen_vel = no ; assign velocities from Maxwell distributiongen_temp = 300 ; temperature for Maxwell distributiongen_seed = -1 ; generate a random seedrefcoord_scaling = com Best regards,Hovakim Grabski -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] gmx energy doesn't calculate LJ-SR and Coul-SR
Dear gromacs users, I ran this tutorial Protein-Ligand Complex with Gromacs 5.1 on a gtx 960 single precision mode. | | | | | | | | | | | Protein-Ligand ComplexThis example will guide a new user through the process of setting up a simulation system containing a protein (T4 lysozyme L99A/M102Q) in complex with a ligand. | | | | Просмотреть на ... | Предварительный просмотр с помощью Yahoo | | | | | But when I use gmx energy to extract Coulomb and LJ, it shows zero:This is the output: Statistics over 51 steps [ 0. through 1000. ps ], 2 data setsAll statistics are over 5001 points Energy Average Err.Est. RMSD Tot-Drift---Coul-SR:Protein-JZ4 0 0 0 0 (kJ/mol)LJ-SR:Protein-JZ4 0 0 0 0 (kJ/mol) This also happens when I run DNA-ligand simulations as well.What can I do?Best regards,Hovakim -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] LIE beta(Van der Waals) term for DNA-ligand interaction
Dear Gromacs users,I'm trying to calculate deltaG for DNA(Dickerson Dodecamer) with Methylene Blue interaction by using LIE(linear interaction energy) method? What would be a good alpha(Coulomb) and beta(Van der Waals) terms values? Best regards,Hovakim -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Make DNA stay in the center of the box during Simulation
Dear Gromacs users,I'm trying to run a simulation between a DNA(12 base pair) and 6 molecules of methylene blue,is there any effective way to make the DNA stay in the center of the box during md simulation? Thanks in advance,Hovakim -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] GROM v0.6 Release Notes
Dear Gromacs users, GROM editor has been updated to version 0.6 and it includes New Features: Major Changes 1. Includes Spelling Suggestion of mdp parameters in context Menu. 2. Includes function to find parameter in Help file 3. Includes Line Number Area 4. Now supports .gro format Fixes 1. replace and search functions 2. all Keyboard Shortcuts function normally 3. fixed zooming function I'll be very grateful to everyone for his comments and suggestions. Send your suggestions to: grom-edi...@googlegroups.com or to my email. Screenshots: https://github.com/hovo1990/GROM/blob/master/README.md Source Code: https://github.com/hovo1990/GROM Thanks in advance, Hovakim Grabski -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] GROM (.mdp, .itp, .top) and .pdb Editor with Syntax Highlighting
Hi Alexander, Since you're using Ubuntu 14.04 32 bit, that would explain why there's an error. I freezed the scripts under 64 bit system. And for the source, I've updated source code's readme file, run: sudo apt-get install libqt5webkit5 sudo apt-get install python3-pyqt5.qtwebkit Best regards, Hovakim среда, 3 сентября 2014 20:55 Александр Селютин saga1...@gmail.com писал(а): It is Great idea but I have some errors with binary ./GROM bash: ./GROM: cannot execute binary file: Ошибка формата выполняемого файла - II don't know how it should look in english but google translate said, that bash: ./GROM: cannot execute binary file: Format error executable with source GROM-master$ python3 GROM.py Traceback (most recent call last): File GROM.py, line 56, in module import grom File /home/user/Загрузки/GROM-master/grom/__init__.py, line 73, in module import PyQt5.QtWebKit ImportError: No module named 'PyQt5.QtWebKit' The packages build-essential python3 qt5-default qttools5-dev-tools python3-pyqt5 were installed before start In the weekend I will run it more carefully I use ubuntu 14.04 32bit -- С уважением, Александр Селютин -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Отв: Отв: GROM (.mdp, .itp, .top) and .pdb Editor with Syntax Highlighting
Hi Alexander, I've updated the Source Code, now it's fixed. Hovakim среда, 3 сентября 2014 21:53 Александр Селютин saga1...@gmail.com писал(а): Thanks! Now it's all right. When I run binary, I lose row where you say that you use 64 bin. Some time ago, I had similar idea, but I wanted to write extension to geany, Very useful idea is the right column with documentation! I test program. I see some strange things. In the mdb files after zoom and unzoom the format is changed to bad. -- С уважением, Александр Селютин -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
