Re: [gmx-users] mdrun -nsteps
Alright, thanks! Am 17.02.2015 13:48, schrieb Mark Abraham: Hi, The second call to mdrun will run 1 steps if it can. Whether that is a continuation or not depends what checkpoint mdrun finds, etc. gmx mdrun -h says -nsteps Run this number of steps, overrides .mdp option This is true, from the point of view of the next MD simulation part, which is what mdrun does. That this part is just one piece of a bigger picture isn't something mdrun needs to help you manage, I think. Using the word append would be ambiguous, because gmx mdrun -append refers to running some number of steps and concatenating the output files (or not, with -noappend). Continue doesn't fully work either, because it implies the existence of a previous simulation part. The main alternative would be defining -nsteps as do this total number of steps, starting from the checkpoint (if any). This isn't very usable unless you know for sure what is in your checkpoint. The current meaning for -nsteps means that it is easy to write a job submission script e.g. for 2 hours doing 50,000 more steps - which is awkward otherwise. Cheers, Mark On Tue, Feb 17, 2015 at 12:10 PM, Sabine Reisser sabine.reis...@kit.edu wrote: Hi, just to be sure: is it intended, that the -nsteps option in mdrun (which is a great feature in general!) actually appends the given number of steps rather than overriding the mdp option? This is what I do: - grompp with mdp file with 5000 steps - mdrun - mdrun -nsteps 1 steps The second mdrun runs until 15000 steps, not 1 steps. Is this intended? If yes, the option description is somewhat misleading. Cheers Sabine -- Dipl. Phys. Sabine Reißer Karlsruhe Institute of Technology (KIT) Institute of Physical Chemistry Phone +49 (0) 721 / 608-45070 -- 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. -- Dipl. Phys. Sabine Reißer Karlsruhe Institute of Technology (KIT) Institute of Physical Chemistry Phone +49 (0) 721 / 608-45070 -- 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.
Re: [gmx-users] GPU low performance
Dear all, the full log file is too big. However in the middle part of it, there are only informations about the energies at each time. The first part is alrady posted. So I post the final part of it: - Step Time Lambda 10002.00.0 Writing checkpoint, step 1000 at Mon Dec 29 13:16:22 2014 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 9.34206e+034.14342e+032.79172e+03 -1.75465e+027.99811e+04 LJ (SR) Coulomb (SR) Coul. recip. PotentialKinetic En. 1.01135e+06 -7.13064e+062.01349e+04 -6.00306e+061.08201e+06 Total Energy Conserved En.Temperature Pressure (bar) Constr. rmsd -4.92106e+06 -5.86747e+062.99426e+021.29480e+022.16280e-05 == ### == A V E R A G E S == ### == Statistics over 1001 steps using 1001 frames Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 9.45818e+034.30665e+032.92407e+03 -1.75556e+028.02473e+04 LJ (SR) Coulomb (SR) Coul. recip. PotentialKinetic En. 1.01284e+06 -7.13138e+062.01510e+04 -6.00163e+061.08407e+06 Total Energy Conserved En.Temperature Pressure (bar) Constr. rmsd -4.91756e+06 -5.38519e+062.8e+021.37549e+020.0e+00 Total Virial (kJ/mol) 3.42887e+051.63625e+011.23658e+02 1.67406e+013.42916e+05 -4.27834e+01 1.23997e+02 -4.29636e+013.42881e+05 Pressure (bar) 1.37573e+027.50214e-02 -1.03916e-01 7.22048e-021.37623e+02 -1.66417e-02 -1.06444e-01 -1.52990e-021.37453e+02 M E G A - F L O P S A C C O U N T I N G NB=Group-cutoff nonbonded kernelsNxN=N-by-N cluster Verlet kernels RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table W3=SPC/TIP3p W4=TIP4p (single or pairs) VF=Potential and force V=Potential only F=Force only Computing: M-Number M-Flops % Flops - Pair Search distance check16343508.605344 147091577.448 0.0 NxN Ewald Elec. + LJ [VF] 5072118956.506304 542716728346.17498.1 1,4 nonbonded interactions 95860.009586 8627400.863 0.0 Calc Weights 13039741.303974 469430686.943 0.1 Spread Q Bspline 278181147.818112 556362295.636 0.1 Gather F Bspline 278181147.818112 1669086886.909 0.3 3D-FFT 880787450.909824 7046299607.279 1.3 Solve PME 163837.90950410485626.208 0.0 Shift-X 108664.934658 651989.608 0.0 Angles 86090.00860914463121.446 0.0 Propers 31380.003138 7186020.719 0.0 Impropers28790.002879 5988320.599 0.0 Virial 4347030.43470378246547.825 0.0 Stop-CM4346580.86931643465808.693 0.0 Calc-Ekin 4346580.869316 117357683.472 0.0 Lincs59130.017739 3547801.064 0.0 Lincs-Mat 1033080.309924 4132321.240 0.0 Constraint-V 4406580.88131635252647.051 0.0 Constraint-Vir 4347450.434745 104338810.434 0.0 Settle 1429440.428832 461709258.513 0.1 - Total 553500452758.122 100.0 - 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 On 1 MPI rank, each using 32 OpenMP threads Computing: Num Num CallWall time Giga-Cycles Ranks Threads Count (s) total sum% - Neighbor search1 32 2500016231.657 518475.694 1.1 Launch GPU ops.1 32 10011825.689 151897.833 0.3 Force 1 32 1001 49568.9594124152.027 8.4 PME mesh 1 32 1001 194798.850 16207321.863 32.8 Wait GPU local 1 32 1001 170272.438 14166717.115 28.7 NB X/F buffer ops. 1 32 19750001 29175.6322427421.177 4.9 Write traj.1 32 206351567.928 130452.056 0.3 Update 1 32 1001 13312.8191107630.452 2.2
Re: [gmx-users] GPU low performance
On Wed, Feb 18, 2015 at 5:57 PM, Carmen Di Giovanni cdigi...@unina.it wrote: Dear all, the full log file is too big. Use pastebin or similar services. However in the middle part of it, there are only informations about the energies at each time. The first part is alrady posted. OK, so first of all, this looks nothing like the alarmingly low CPU-GPU overlap you posted about initially. Here, the GPU you are using simply can't keep up with 2x8 Haswell-E cores. You observing this by looking at the fraction of runtime spent by the CPU waiting for the GPU displayed in the performace table's Wait GPU local row which shows 28.7% idling. At the moment, the non-bonded computation which is fully don on the GPU can't be split between CPU and GPU, so your options are limited and most of these will a minor effect: i) indirectly shift work back to the CPU and/or improve the overlap efficiency a) try decreasing nstlist to 10-20-25 b) run on less threads (as suggested before) which will likely improve performance in some non-overlap code parts c) run with DD, e.g. -ntmpi 4 -ntomp 4/8 -gpu_id 0011 or -ntmpi 8 -gpu_id ii) Reduce the Rest time. Not sure what's causing it, but you simulation spends a substantial amount (15.6%) of the runtime in unaccounted for likely serial calculation; i-b and i-c will likely reduce this somewhat too; iii) get more/faster or GPUs So I post the final part of it: - Step Time Lambda 10002.00.0 Writing checkpoint, step 1000 at Mon Dec 29 13:16:22 2014 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 9.34206e+034.14342e+032.79172e+03 -1.75465e+027.99811e+04 LJ (SR) Coulomb (SR) Coul. recip. PotentialKinetic En. 1.01135e+06 -7.13064e+062.01349e+04 -6.00306e+061.08201e+06 Total Energy Conserved En.Temperature Pressure (bar) Constr. rmsd -4.92106e+06 -5.86747e+062.99426e+021.29480e+022.16280e-05 == ### == A V E R A G E S == ### == Statistics over 1001 steps using 1001 frames Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 9.45818e+034.30665e+032.92407e+03 -1.75556e+028.02473e+04 LJ (SR) Coulomb (SR) Coul. recip. PotentialKinetic En. 1.01284e+06 -7.13138e+062.01510e+04 -6.00163e+061.08407e+06 Total Energy Conserved En.Temperature Pressure (bar) Constr. rmsd -4.91756e+06 -5.38519e+062.8e+021.37549e+020.0e+00 Total Virial (kJ/mol) 3.42887e+051.63625e+011.23658e+02 1.67406e+013.42916e+05 -4.27834e+01 1.23997e+02 -4.29636e+013.42881e+05 Pressure (bar) 1.37573e+027.50214e-02 -1.03916e-01 7.22048e-021.37623e+02 -1.66417e-02 -1.06444e-01 -1.52990e-021.37453e+02 M E G A - F L O P S A C C O U N T I N G NB=Group-cutoff nonbonded kernelsNxN=N-by-N cluster Verlet kernels RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table W3=SPC/TIP3p W4=TIP4p (single or pairs) VF=Potential and force V=Potential only F=Force only Computing: M-Number M-Flops % Flops - Pair Search distance check16343508.605344 147091577.448 0.0 NxN Ewald Elec. + LJ [VF] 5072118956.506304 542716728346.17498.1 1,4 nonbonded interactions 95860.009586 8627400.863 0.0 Calc Weights 13039741.303974 469430686.943 0.1 Spread Q Bspline 278181147.818112 556362295.636 0.1 Gather F Bspline 278181147.818112 1669086886.909 0.3 3D-FFT 880787450.909824 7046299607.279 1.3 Solve PME 163837.90950410485626.208 0.0 Shift-X 108664.934658 651989.608 0.0 Angles 86090.00860914463121.446 0.0 Propers 31380.003138 7186020.719 0.0 Impropers28790.002879 5988320.599 0.0 Virial 4347030.43470378246547.825 0.0 Stop-CM4346580.86931643465808.693 0.0 Calc-Ekin 4346580.869316 117357683.472 0.0 Lincs59130.017739 3547801.064 0.0 Lincs-Mat 1033080.309924 4132321.240 0.0 Constraint-V 4406580.88131635252647.051 0.0 Constraint-Vir 4347450.434745
Re: [gmx-users] GPU low performance
I've just noticed something serious. Why are you calculating energies every step? Doing that makes the non-bonded force calculation on average 25-30% slower than e.g. calculating energies every 100-th step. You may be able to get another 5% or so form your GPU, could you post the output of nvidia-smi -q -g 0? -- Szilárd On Wed, Feb 18, 2015 at 6:14 PM, Szilárd Páll pall.szil...@gmail.com wrote: On Wed, Feb 18, 2015 at 5:57 PM, Carmen Di Giovanni cdigi...@unina.it wrote: Dear all, the full log file is too big. Use pastebin or similar services. However in the middle part of it, there are only informations about the energies at each time. The first part is alrady posted. OK, so first of all, this looks nothing like the alarmingly low CPU-GPU overlap you posted about initially. Here, the GPU you are using simply can't keep up with 2x8 Haswell-E cores. You observing this by looking at the fraction of runtime spent by the CPU waiting for the GPU displayed in the performace table's Wait GPU local row which shows 28.7% idling. At the moment, the non-bonded computation which is fully don on the GPU can't be split between CPU and GPU, so your options are limited and most of these will a minor effect: i) indirectly shift work back to the CPU and/or improve the overlap efficiency a) try decreasing nstlist to 10-20-25 b) run on less threads (as suggested before) which will likely improve performance in some non-overlap code parts c) run with DD, e.g. -ntmpi 4 -ntomp 4/8 -gpu_id 0011 or -ntmpi 8 -gpu_id ii) Reduce the Rest time. Not sure what's causing it, but you simulation spends a substantial amount (15.6%) of the runtime in unaccounted for likely serial calculation; i-b and i-c will likely reduce this somewhat too; iii) get more/faster or GPUs So I post the final part of it: - Step Time Lambda 10002.00.0 Writing checkpoint, step 1000 at Mon Dec 29 13:16:22 2014 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 9.34206e+034.14342e+032.79172e+03 -1.75465e+027.99811e+04 LJ (SR) Coulomb (SR) Coul. recip. PotentialKinetic En. 1.01135e+06 -7.13064e+062.01349e+04 -6.00306e+061.08201e+06 Total Energy Conserved En.Temperature Pressure (bar) Constr. rmsd -4.92106e+06 -5.86747e+062.99426e+021.29480e+022.16280e-05 == ### == A V E R A G E S == ### == Statistics over 1001 steps using 1001 frames Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 9.45818e+034.30665e+032.92407e+03 -1.75556e+028.02473e+04 LJ (SR) Coulomb (SR) Coul. recip. PotentialKinetic En. 1.01284e+06 -7.13138e+062.01510e+04 -6.00163e+061.08407e+06 Total Energy Conserved En.Temperature Pressure (bar) Constr. rmsd -4.91756e+06 -5.38519e+062.8e+021.37549e+020.0e+00 Total Virial (kJ/mol) 3.42887e+051.63625e+011.23658e+02 1.67406e+013.42916e+05 -4.27834e+01 1.23997e+02 -4.29636e+013.42881e+05 Pressure (bar) 1.37573e+027.50214e-02 -1.03916e-01 7.22048e-021.37623e+02 -1.66417e-02 -1.06444e-01 -1.52990e-021.37453e+02 M E G A - F L O P S A C C O U N T I N G NB=Group-cutoff nonbonded kernelsNxN=N-by-N cluster Verlet kernels RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table W3=SPC/TIP3p W4=TIP4p (single or pairs) VF=Potential and force V=Potential only F=Force only Computing: M-Number M-Flops % Flops - Pair Search distance check16343508.605344 147091577.448 0.0 NxN Ewald Elec. + LJ [VF] 5072118956.506304 542716728346.17498.1 1,4 nonbonded interactions 95860.009586 8627400.863 0.0 Calc Weights 13039741.303974 469430686.943 0.1 Spread Q Bspline 278181147.818112 556362295.636 0.1 Gather F Bspline 278181147.818112 1669086886.909 0.3 3D-FFT 880787450.909824 7046299607.279 1.3 Solve PME 163837.90950410485626.208 0.0 Shift-X 108664.934658 651989.608 0.0 Angles 86090.00860914463121.446 0.0 Propers 31380.003138 7186020.719 0.0 Impropers28790.002879 5988320.599 0.0 Virial 4347030.43470378246547.825 0.0 Stop-CM
[gmx-users] Need of mdp files
Hi, I am trying to simulate a peripheral membrane protein in a heterogenous lipid bilayer of DOPC and DOPG using charmm 36 force field in GROMACS. i need mdp files for NPT, NVT, steep and MD to check whether the conditions i am using to simulate my system are appropriate or not. -- Regards, Antara -- J.R.F.(Project) Systems Biology Group CSIR - Institute of Genomics Integrative Biology South Campus, New Delhi-110020 M:+91-9717970040 -- -- 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.
Re: [gmx-users] simulation of heme along with h2o2
Dear Justin, thank you for the reply. However, I would like to know if there is any server which can generate parameters for heme to be used in OPLS-aa? We have already tried in swissparam with failed results. Please help. On 18 February 2015 at 21:15, Justin Lemkul jalem...@vt.edu wrote: On 2/18/15 9:18 AM, Sanchaita Rajkhowa wrote: Dear all, I am trying to simulate a heme containing protein in high concentration (having hydrogen peroxide). However, I do not know which forcefield to use. Heme has forcefield in gromos96 but not the forcefield of H2O2? Will generating .itp files for H2O2 from swissparam work? Please help. SwissParam creates CHARMM-compatible parameters, so no, you can't mix those with GROMOS. CHARMM supports heme, but you have to clean up a lot of auto-generated angles and dihedrals that don't belong. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- 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.
Re: [gmx-users] GPU low performance
Justin, the problem is evident for all calculations. This is the log file of a recent run: Log file opened on Mon Dec 22 16:28:00 2014 Host: localhost.localdomain pid: 8378 rank ID: 0 number of ranks: 1 GROMACS:gmx mdrun, VERSION 5.0 GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van DrunenAnton Feenstra Sebastian Fritsch Gerrit GroenhofChristoph Junghans Peter Kasson Carsten Kutzner Per LarssonJustin A. Lemkul Magnus LundborgPieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey ShvetsovMichael Shirts Alfons Sijbers Peter Tieleman Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2014, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, VERSION 5.0 Executable: /opt/SW/gromacs-5.0/build/mpi-cuda/bin/gmx_mpi Library dir: /opt/SW/gromacs-5.0/share/top Command line: gmx_mpi mdrun -deffnm prod_20ns Gromacs version:VERSION 5.0 Precision: single Memory model: 64 bit MPI library:MPI OpenMP support: enabled GPU support:enabled invsqrt routine:gmx_software_invsqrt(x) SIMD instructions: AVX_256 FFT library:fftw-3.3.3-sse2 RDTSCP usage: enabled C++11 compilation: disabled TNG support:enabled Tracing support:disabled Built on: Thu Jul 31 18:30:37 CEST 2014 Built by: root@localhost.localdomain [CMAKE] Build OS/arch: Linux 2.6.32-431.el6.x86_64 x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz Build CPU family: 6 Model: 62 Stepping: 4 Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/bin/cc GNU 4.4.7 C compiler flags:-mavx -Wno-maybe-uninitialized -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -fomit-frame-pointer -funroll-all-loops -Wno-array-bounds -O3 -DNDEBUG C++ compiler: /usr/bin/c++ GNU 4.4.7 C++ compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -fomit-frame-pointer -funroll-all-loops -Wno-array-bounds -O3 -DNDEBUG Boost version: 1.55.0 (internal) CUDA compiler: /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2013 NVIDIA Corporation;Built on Thu_Mar_13_11:58:58_PDT_2014;Cuda compilation tools, release 6.0, V6.0.1 CUDA compiler flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_20,code=sm_21;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_35,code=compute_35;-use_fast_math;-Xcompiler;-fPIC ; ;-mavx;-Wextra;-Wno-missing-field-initializers;-Wpointer-arith;-Wall;-Wno-unused-function;-fomit-frame-pointer;-funroll-all-loops;-Wno-array-bounds;-O3;-DNDEBUG CUDA driver:6.50 CUDA runtime: 6.0 PLEASE READ AND CITE THE FOLLOWING REFERENCE B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 435-447 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen GROMACS: Fast, Flexible and Free J. Comp. Chem. 26 (2005) pp. 1701-1719 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE E. Lindahl and B. Hess and D. van der Spoel GROMACS 3.0: A package for molecular simulation and trajectory analysis J. Mol. Mod. 7 (2001) pp. 306-317 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE H. J. C. Berendsen, D. van der Spoel and R. van Drunen GROMACS: A message-passing parallel molecular dynamics implementation Comp. Phys. Comm. 91 (1995) pp. 43-56 --- Thank You --- For optimal performance with a GPU nstlist (now 10) should be larger. The optimum depends on your CPU and GPU resources. You
Re: [gmx-users] GPU low performance
On 2/18/15 11:20 AM, Carmen Di Giovanni wrote: Justin, the problem is evident for all calculations. This is the log file of a recent run: Again, this is *part* of a .log file, but at least we're starting to get somewhere. Please realize that I'm not insisting on this for no reason; there is critical information in the last part of the .log file! We know what we're looking for - please give it to us so we can help! A few things: GROMACS:gmx mdrun, VERSION 5.0 Upgrade to 5.0.4 to avoid some GPU-specific bugs. See the release notes. snip Using 1 MPI process Using 32 OpenMP threads As was pointed out earlier, there is a lot of fine-tuning that can try to improve performance. mdrun tries to guess what will be best for your hardware, but it's not always right. See the linked page that was posted before, as well as the numerous discussions about improving GPU performance. snip System total charge: -0.012 Check your topology; something might be wrong here. snip There are: 434658 Atoms Pretty big system, so you *might* be getting as good of performance as you can expect from the hardware. snip There's important stuff you're leaving out here :) -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] simulation of heme along with h2o2
Dear all, I am trying to simulate a heme containing protein in high concentration (having hydrogen peroxide). However, I do not know which forcefield to use. Heme has forcefield in gromos96 but not the forcefield of H2O2? Will generating .itp files for H2O2 from swissparam work? Please help. Thanks in advance. Sanchaita. -- 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.
Re: [gmx-users] free energy calculation: combination of position restraint +refcoord_scaling cause crash during NPT
On 2/17/15 12:31 PM, Jin Zhang wrote:
Dear all,
We're doing free energy calculation and found some of my lambda job crashes
due to the combination of position restraint +refcoord_scaling COM. All
crashes happened at NPT steps.
By checking each energy term, we found the Position Rest. term is
surprisingly as high as 10^6 kJ/mol, the others look fine. Either turn of
position restrain or refcoord_scaling could avoid the simulation to be
crashed. We tried to see if there's mismatch of either COM or coordinate
and found no direct answer.
Any help would be appreciated!
In the tpr file
refcoord-scaling = COM
posres-com (3):
posres-com[0]= 3.15034e-01
posres-com[1]= 4.48110e-01
posres-com[2]= 5.17730e-01
COM of protein-ligand calculated by t_traj -com -ox
3.024224.301694.84964
If the reference COM is defined as (0.315,0.448,0.518) and your actual
coordinates are what you're shown above, there will inherently be a huge
restraint potential as mdrun tries to bias the coordinates towards the defined
reference. I suspect something is wrong in your definition of your reference.
-Justin
coordinate of 1st atom in tpr: posres_xA[0]={ 1.39783e-01,
-9.56922e-02, 1.22536e+00}
coordinate of 1st atom in gro: 1MOL C11 3.164 4.206
6.075
The same thing was also found in a normal non-free energy simulations with
combination of position restrain and refcoord-scaling.
Later on, we found some other people also have the same problem when use
that combination to do free energy calculation.
http://comments.gmane.org/gmane.science.biology.gromacs.user/66177
It makes more sense to me to turn on refcoord_scaling while using position
restraint.
Again, any help to understand this would be appreciated!
Regards,
Jin
--
==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
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Re: [gmx-users] Double counting of h-bonds g_hbond:issue
On 2/17/15 5:14 PM, Udaya Dahal wrote: Thanks Justin for prompt reply. Actually I calculated for the h_bonds with same criteria for (angle 30 and distance(D-A) 0.35nm) from VMD, and the number is lot less for both Polymer water and water water. I have 193 water molecules and the H-bond from VMD with same criteria gives me 232 H-bonds while GROMACS provides 340. The value GROMACS provides is better in the sense that it matches more closely to the experimental value but I kind of unsure since the visualization (in VMD ) also showed very few bonds. It shows like only 5 bonds from vmd calculation(and visualization) in previously mentioned Polymer water h-bonds. Probably VMD's plugin and g_hbond are doing something different. Note the VMD documentation seems to indicate the angle criteria is defined differently (D-H-A angle whereas g_hbond uses H-D-A, yet they use a similar value as a cutoff). Define a very small test system, something that you can literally look at and know the answer for sure, and see if the two programs agree. -Justin On Tue, Feb 17, 2015 at 7:58 AM, Justin Lemkul jalem...@vt.edu wrote: On 2/16/15 7:39 PM, Udaya Dahal wrote: Hi All, When I used the g_hbond the hydrogen bonding i was getting was quite good but when I checked the index file i find double counting of the bonds. So far, it seems to me that g_hbond is giving higher than the real hydrogen bonds present in the system. For eg. in the following OW-HW-oxygen, we see there are two bonds between 109(OW) and 110(HW) for two different polymer oxygens. Can anyone explain this issue? 76 77 12 100101 47 109110 40---1 (same hydrogen with two different oxygens) 109110 54---2(same hydrogen with two different oxygens) So does a visual inspection of this particular frame confirm that there shouldn't actually be hydrogen bonds with these atoms? This isn't double-counting, it's just a bit unusual, but is possible within the context of whatever criteria you have set for defining a hydrogen bond. -Justin 211212 54 211212 68 337338 68 343344 5 343344 19 403404 61 487488 5 511512 26 511512 40 538539 33 592593 12 592593 26 Hbnum.xvg shows hydrogen bonds pairs within 0.35 16 8 Regards, Udaya -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
Re: [gmx-users] GPU low performance
I post the message of a md run : Force evaluation time GPU/CPU: 40.974 ms/24.437 ms = 1.677 For optimal performance this ratio should be close to 1! NOTE: The GPU has 20% more load than the CPU. This imbalance causes performance loss, consider using a shorter cut-off and a finer PME grid. As can I solved this problem ? Thank you in advance -- Carmen Di Giovanni, PhD Dept. of Pharmaceutical and Toxicological Chemistry Drug Discovery Lab University of Naples Federico II Via D. Montesano, 49 80131 Naples Tel.: ++39 081 678623 Fax: ++39 081 678100 Email: cdigi...@unina.it Quoting Justin Lemkul jalem...@vt.edu: On 2/18/15 10:30 AM, Carmen Di Giovanni wrote: Daear all, I'm working on a machine with an INVIDIA Teska K20. After a minimization on a protein of 1925 atoms this is the mesage: Force evaluation time GPU/CPU: 2.923 ms/116.774 ms = 0.025 For optimal performance this ratio should be close to 1! Minimization is a poor indicator of performance. Do a real MD run. NOTE: The GPU has 25% less load than the CPU. This imbalance causes performance loss. Core t (s) Wall t (s) (%) Time: 3289.010 205.891 1597.4 (steps/hour) Performance: 8480.2 Finished mdrun on rank 0 Wed Feb 18 15:50:06 2015 Cai I improve the performance? At the moment in the forum I didn't full informations to solve this problem. In attachment there is the log. file The list does not accept attachments. If you wish to share a file, upload it to a file-sharing service and provide a URL. The full .log is quite important for understanding your hardware, optimizations, and seeing full details of the performance breakdown. But again, base your assessment on MD, not EM. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- 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.
Re: [gmx-users] GPU low performance
What's your exact command? Have you reviewed this page: http://www.gromacs.org/Documentation/Acceleration_and_parallelization James Wes Barnett Ph.D. Candidate Chemical and Biomolecular Engineering Tulane University Boggs Center for Energy and Biotechnology, Room 341-B From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Carmen Di Giovanni cdigi...@unina.it Sent: Wednesday, February 18, 2015 10:06 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] GPU low performance I post the message of a md run : Force evaluation time GPU/CPU: 40.974 ms/24.437 ms = 1.677 For optimal performance this ratio should be close to 1! NOTE: The GPU has 20% more load than the CPU. This imbalance causes performance loss, consider using a shorter cut-off and a finer PME grid. As can I solved this problem ? Thank you in advance -- Carmen Di Giovanni, PhD Dept. of Pharmaceutical and Toxicological Chemistry Drug Discovery Lab University of Naples Federico II Via D. Montesano, 49 80131 Naples Tel.: ++39 081 678623 Fax: ++39 081 678100 Email: cdigi...@unina.it Quoting Justin Lemkul jalem...@vt.edu: On 2/18/15 10:30 AM, Carmen Di Giovanni wrote: Daear all, I'm working on a machine with an INVIDIA Teska K20. After a minimization on a protein of 1925 atoms this is the mesage: Force evaluation time GPU/CPU: 2.923 ms/116.774 ms = 0.025 For optimal performance this ratio should be close to 1! Minimization is a poor indicator of performance. Do a real MD run. NOTE: The GPU has 25% less load than the CPU. This imbalance causes performance loss. Core t (s) Wall t (s) (%) Time: 3289.010 205.891 1597.4 (steps/hour) Performance: 8480.2 Finished mdrun on rank 0 Wed Feb 18 15:50:06 2015 Cai I improve the performance? At the moment in the forum I didn't full informations to solve this problem. In attachment there is the log. file The list does not accept attachments. If you wish to share a file, upload it to a file-sharing service and provide a URL. The full .log is quite important for understanding your hardware, optimizations, and seeing full details of the performance breakdown. But again, base your assessment on MD, not EM. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- 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. -- 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.
Re: [gmx-users] GPU low performance
On 2/18/15 11:09 AM, Barnett, James W wrote: What's your exact command? A full .log file would be even better; it would tell us everything we need to know :) -Justin Have you reviewed this page: http://www.gromacs.org/Documentation/Acceleration_and_parallelization James Wes Barnett Ph.D. Candidate Chemical and Biomolecular Engineering Tulane University Boggs Center for Energy and Biotechnology, Room 341-B From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Carmen Di Giovanni cdigi...@unina.it Sent: Wednesday, February 18, 2015 10:06 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] GPU low performance I post the message of a md run : Force evaluation time GPU/CPU: 40.974 ms/24.437 ms = 1.677 For optimal performance this ratio should be close to 1! NOTE: The GPU has 20% more load than the CPU. This imbalance causes performance loss, consider using a shorter cut-off and a finer PME grid. As can I solved this problem ? Thank you in advance -- Carmen Di Giovanni, PhD Dept. of Pharmaceutical and Toxicological Chemistry Drug Discovery Lab University of Naples Federico II Via D. Montesano, 49 80131 Naples Tel.: ++39 081 678623 Fax: ++39 081 678100 Email: cdigi...@unina.it Quoting Justin Lemkul jalem...@vt.edu: On 2/18/15 10:30 AM, Carmen Di Giovanni wrote: Daear all, I'm working on a machine with an INVIDIA Teska K20. After a minimization on a protein of 1925 atoms this is the mesage: Force evaluation time GPU/CPU: 2.923 ms/116.774 ms = 0.025 For optimal performance this ratio should be close to 1! Minimization is a poor indicator of performance. Do a real MD run. NOTE: The GPU has 25% less load than the CPU. This imbalance causes performance loss. Core t (s) Wall t (s) (%) Time: 3289.010 205.891 1597.4 (steps/hour) Performance: 8480.2 Finished mdrun on rank 0 Wed Feb 18 15:50:06 2015 Cai I improve the performance? At the moment in the forum I didn't full informations to solve this problem. In attachment there is the log. file The list does not accept attachments. If you wish to share a file, upload it to a file-sharing service and provide a URL. The full .log is quite important for understanding your hardware, optimizations, and seeing full details of the performance breakdown. But again, base your assessment on MD, not EM. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
Re: [gmx-users] GPU low performance
Dear James, this is the command: gmx_mpi mdrun -s prod_30ns.tpr -deffnm prod_30ns -gpu_id 0 where gpu_id = 0 is INVIDIA Tesla K20 -- Carmen Di Giovanni, PhD Dept. of Pharmaceutical and Toxicological Chemistry Drug Discovery Lab University of Naples Federico II Via D. Montesano, 49 80131 Naples Tel.: ++39 081 678623 Fax: ++39 081 678100 Email: cdigi...@unina.it Quoting Barnett, James W jbarn...@tulane.edu: What's your exact command? Have you reviewed this page: http://www.gromacs.org/Documentation/Acceleration_and_parallelization James Wes Barnett Ph.D. Candidate Chemical and Biomolecular Engineering Tulane University Boggs Center for Energy and Biotechnology, Room 341-B From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Carmen Di Giovanni cdigi...@unina.it Sent: Wednesday, February 18, 2015 10:06 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] GPU low performance I post the message of a md run : Force evaluation time GPU/CPU: 40.974 ms/24.437 ms = 1.677 For optimal performance this ratio should be close to 1! NOTE: The GPU has 20% more load than the CPU. This imbalance causes performance loss, consider using a shorter cut-off and a finer PME grid. As can I solved this problem ? Thank you in advance -- Carmen Di Giovanni, PhD Dept. of Pharmaceutical and Toxicological Chemistry Drug Discovery Lab University of Naples Federico II Via D. Montesano, 49 80131 Naples Tel.: ++39 081 678623 Fax: ++39 081 678100 Email: cdigi...@unina.it Quoting Justin Lemkul jalem...@vt.edu: On 2/18/15 10:30 AM, Carmen Di Giovanni wrote: Daear all, I'm working on a machine with an INVIDIA Teska K20. After a minimization on a protein of 1925 atoms this is the mesage: Force evaluation time GPU/CPU: 2.923 ms/116.774 ms = 0.025 For optimal performance this ratio should be close to 1! Minimization is a poor indicator of performance. Do a real MD run. NOTE: The GPU has 25% less load than the CPU. This imbalance causes performance loss. Core t (s) Wall t (s) (%) Time: 3289.010 205.891 1597.4 (steps/hour) Performance: 8480.2 Finished mdrun on rank 0 Wed Feb 18 15:50:06 2015 Cai I improve the performance? At the moment in the forum I didn't full informations to solve this problem. In attachment there is the log. file The list does not accept attachments. If you wish to share a file, upload it to a file-sharing service and provide a URL. The full .log is quite important for understanding your hardware, optimizations, and seeing full details of the performance breakdown. But again, base your assessment on MD, not EM. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- 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. -- 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. -- 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] GPU low performance
Daear all, I'm working on a machine with an INVIDIA Teska K20. After a minimization on a protein of 1925 atoms this is the mesage: Force evaluation time GPU/CPU: 2.923 ms/116.774 ms = 0.025 For optimal performance this ratio should be close to 1! NOTE: The GPU has 25% less load than the CPU. This imbalance causes performance loss. Core t (s) Wall t (s) (%) Time: 3289.010 205.891 1597.4 (steps/hour) Performance: 8480.2 Finished mdrun on rank 0 Wed Feb 18 15:50:06 2015 Cai I improve the performance? At the moment in the forum I didn't full informations to solve this problem. In attachment there is the log. file thank you in advance Carmen Di Giovanni -- Carmen Di Giovanni, PhD Dept. of Pharmaceutical and Toxicological Chemistry Drug Discovery Lab University of Naples Federico II Via D. Montesano, 49 80131 Naples Tel.: ++39 081 678623 Fax: ++39 081 678100 Email: cdigi...@unina.it Carmen Di Giovanni, PhD Postdoctoral Researcher Dept. of Pharmacy Drug Discovery Lab University of Naples Federico II Via D. Montesano, 49 80131 Naples Tel.: ++39 081 678623 Fax: ++39 081 678100 Email: cdigi...@unina.it -- 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.
Re: [gmx-users] simulation of heme along with h2o2
On 2/18/15 9:18 AM, Sanchaita Rajkhowa wrote: Dear all, I am trying to simulate a heme containing protein in high concentration (having hydrogen peroxide). However, I do not know which forcefield to use. Heme has forcefield in gromos96 but not the forcefield of H2O2? Will generating .itp files for H2O2 from swissparam work? Please help. SwissParam creates CHARMM-compatible parameters, so no, you can't mix those with GROMOS. CHARMM supports heme, but you have to clean up a lot of auto-generated angles and dihedrals that don't belong. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
Re: [gmx-users] GPU low performance
On 2/18/15 10:30 AM, Carmen Di Giovanni wrote: Daear all, I'm working on a machine with an INVIDIA Teska K20. After a minimization on a protein of 1925 atoms this is the mesage: Force evaluation time GPU/CPU: 2.923 ms/116.774 ms = 0.025 For optimal performance this ratio should be close to 1! Minimization is a poor indicator of performance. Do a real MD run. NOTE: The GPU has 25% less load than the CPU. This imbalance causes performance loss. Core t (s) Wall t (s) (%) Time: 3289.010 205.891 1597.4 (steps/hour) Performance: 8480.2 Finished mdrun on rank 0 Wed Feb 18 15:50:06 2015 Cai I improve the performance? At the moment in the forum I didn't full informations to solve this problem. In attachment there is the log. file The list does not accept attachments. If you wish to share a file, upload it to a file-sharing service and provide a URL. The full .log is quite important for understanding your hardware, optimizations, and seeing full details of the performance breakdown. But again, base your assessment on MD, not EM. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
Re: [gmx-users] GPU low performance
We need a *full* log file, not parts of it! You can try running with -ntomp 16 -pin on - it may be a bit faster not not use HyperThreading. -- Szilárd On Wed, Feb 18, 2015 at 5:20 PM, Carmen Di Giovanni cdigi...@unina.it wrote: Justin, the problem is evident for all calculations. This is the log file of a recent run: Log file opened on Mon Dec 22 16:28:00 2014 Host: localhost.localdomain pid: 8378 rank ID: 0 number of ranks: 1 GROMACS:gmx mdrun, VERSION 5.0 GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van DrunenAnton Feenstra Sebastian Fritsch Gerrit GroenhofChristoph Junghans Peter Kasson Carsten Kutzner Per LarssonJustin A. Lemkul Magnus LundborgPieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey ShvetsovMichael Shirts Alfons Sijbers Peter Tieleman Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2014, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, VERSION 5.0 Executable: /opt/SW/gromacs-5.0/build/mpi-cuda/bin/gmx_mpi Library dir: /opt/SW/gromacs-5.0/share/top Command line: gmx_mpi mdrun -deffnm prod_20ns Gromacs version:VERSION 5.0 Precision: single Memory model: 64 bit MPI library:MPI OpenMP support: enabled GPU support:enabled invsqrt routine:gmx_software_invsqrt(x) SIMD instructions: AVX_256 FFT library:fftw-3.3.3-sse2 RDTSCP usage: enabled C++11 compilation: disabled TNG support:enabled Tracing support:disabled Built on: Thu Jul 31 18:30:37 CEST 2014 Built by: root@localhost.localdomain [CMAKE] Build OS/arch: Linux 2.6.32-431.el6.x86_64 x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz Build CPU family: 6 Model: 62 Stepping: 4 Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/bin/cc GNU 4.4.7 C compiler flags:-mavx -Wno-maybe-uninitialized -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -fomit-frame-pointer -funroll-all-loops -Wno-array-bounds -O3 -DNDEBUG C++ compiler: /usr/bin/c++ GNU 4.4.7 C++ compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -fomit-frame-pointer -funroll-all-loops -Wno-array-bounds -O3 -DNDEBUG Boost version: 1.55.0 (internal) CUDA compiler: /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2013 NVIDIA Corporation;Built on Thu_Mar_13_11:58:58_PDT_2014;Cuda compilation tools, release 6.0, V6.0.1 CUDA compiler flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_20,code=sm_21;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_35,code=compute_35;-use_fast_math;-Xcompiler;-fPIC ; ;-mavx;-Wextra;-Wno-missing-field-initializers;-Wpointer-arith;-Wall;-Wno-unused-function;-fomit-frame-pointer;-funroll-all-loops;-Wno-array-bounds;-O3;-DNDEBUG CUDA driver:6.50 CUDA runtime: 6.0 PLEASE READ AND CITE THE FOLLOWING REFERENCE B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 435-447 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen GROMACS: Fast, Flexible and Free J. Comp. Chem. 26 (2005) pp. 1701-1719 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE E. Lindahl and B. Hess and D. van der Spoel GROMACS 3.0: A package for molecular simulation and trajectory analysis J. Mol. Mod. 7 (2001) pp. 306-317 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE H. J. C. Berendsen, D. van der Spoel and R. van
Re: [gmx-users] free energy calculation: combination of position restraint +refcoord_scaling cause crash during NPT (Justin Lemkul)
Dear Justin,
We thought about this, and checked these non-crashed lambda tpr as well as
the pre-equilbrated NPT step, all showed mismatch between posre-com[0]
posre-com[1] posre-com[2], and the real com. So I suspect this posre-com is
not the real center of mass for NPT simulation.
Since the reference coordinate is read from -c .gro when perform grompp, it
should not be wrong, unless it read elsewhere.
Best,
Jin
Date: Wed, 18 Feb 2015 07:42:30 -0500
From: Justin Lemkul jalem...@vt.edu
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] free energy calculation: combination of
position restraint +refcoord_scaling cause crash during NPT
Message-ID: 54e488b6.9090...@vt.edu
Content-Type: text/plain; charset=windows-1252; format=flowed
On 2/17/15 12:31 PM, Jin Zhang wrote:
Dear all,
We're doing free energy calculation and found some of my lambda job
crashes
due to the combination of position restraint +refcoord_scaling COM. All
crashes happened at NPT steps.
By checking each energy term, we found the Position Rest. term is
surprisingly as high as 10^6 kJ/mol, the others look fine. Either turn of
position restrain or refcoord_scaling could avoid the simulation to be
crashed. We tried to see if there's mismatch of either COM or coordinate
and found no direct answer.
Any help would be appreciated!
In the tpr file
refcoord-scaling = COM
posres-com (3):
posres-com[0]= 3.15034e-01
posres-com[1]= 4.48110e-01
posres-com[2]= 5.17730e-01
COM of protein-ligand calculated by t_traj -com -ox
3.024224.301694.84964
If the reference COM is defined as (0.315,0.448,0.518) and your actual
coordinates are what you're shown above, there will inherently be a huge
restraint potential as mdrun tries to bias the coordinates towards the
defined
reference. I suspect something is wrong in your definition of your
reference.
-Justin
coordinate of 1st atom in tpr: posres_xA[0]={ 1.39783e-01,
-9.56922e-02, 1.22536e+00}
coordinate of 1st atom in gro: 1MOL C11 3.164 4.206
6.075
The same thing was also found in a normal non-free energy simulations
with
combination of position restrain and refcoord-scaling.
Later on, we found some other people also have the same problem when use
that combination to do free energy calculation.
http://comments.gmane.org/gmane.science.biology.gromacs.user/66177
It makes more sense to me to turn on refcoord_scaling while using
position
restraint.
Again, any help to understand this would be appreciated!
Regards,
Jin
--
==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
--
Message: 3
Date: Wed, 18 Feb 2015 19:48:50 +0530
From: Sanchaita Rajkhowa srajkhow...@gmail.com
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] simulation of heme along with h2o2
Message-ID:
CACE5zdsaXX==in=SPntZiaRZ=+
nrjnyajn8uwmmwysvsr4x...@mail.gmail.com
Content-Type: text/plain; charset=UTF-8
Dear all, I am trying to simulate a heme containing protein in high
concentration (having hydrogen peroxide). However, I do not know which
forcefield to use. Heme has forcefield in gromos96 but not the forcefield
of H2O2? Will generating .itp files for H2O2 from swissparam work? Please
help.
Thanks in advance.
Sanchaita.
--
Message: 4
Date: Wed, 18 Feb 2015 16:30:34 +0100
From: Carmen Di Giovanni cdigi...@unina.it
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] GPU low performance
Message-ID: 8525B4BE52BB4609BCED7556FAFB3587@PCCarmen
Content-Type: text/plain; charset=iso-8859-1
Daear all,
I'm working on a machine with an INVIDIA Teska K20.
After a minimization on a protein of 1925 atoms this is the mesage:
Force evaluation time GPU/CPU: 2.923 ms/116.774 ms = 0.025
For optimal performance this ratio should be close to 1!
NOTE: The GPU has 25% less load than the CPU. This imbalance causes
performance loss.
Core t (s) Wall t (s) (%)
Time: 3289.010 205.891 1597.4
(steps/hour)
Performance: 8480.2
Finished mdrun on rank 0 Wed Feb 18 15:50:06 2015
Cai I improve the performance?
At the moment in the forum I didn't full informations to solve this
problem.
In attachment there is the log. file
thank you in advance
Carmen Di Giovanni
--
Carmen Di Giovanni, PhD
Dept. of Pharmaceutical and Toxicological Chemistry
Drug Discovery Lab
University of Naples Federico II
Via D. Montesano, 49
80131 Naples
Tel.: ++39 081 678623
Fax: ++39 081
