Re: [gmx-users] Best force Field for Protein
Justn, >Then there are force fields that do better than others, but >the choice must be yours based on a thorough review of available >literature; Can you provide a list of FFs more suitable for folding and IDP simulations? Thank you, Dmytro From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: Monday, November 19, 2018 5:46 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Best force Field for Protein On 11/18/18 10:46 AM, Edjan Silva wrote: > Dear Gromacs users, I will perform a simulation of a protein with explicit > solvent to verify structural changes in temperatures of 300 k and 310 k. I doubt any force field will give you any meaningful differences at such a small temperature interval. > Given the various force fields available on the gromacs platform, which one > would be most appropriate for my experiment? There's no real way to know. Different force fields do well at different things. Simulating "a protein" can mean a lot of different things. Are you simulating a well-folded protein with a stable tertiary structure? If so, just about any modern force field will perform equivalently. Are you trying to fold a protein or simulate something intrinsically disordered? Then there are force fields that do better than others, but the choice must be yours based on a thorough review of available literature; it's not something that strangers on an Internet forum can conclude for you :) -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] Running GPU issue
The error you saw is clear evidence of a bug. There's a few things you might try to help narrow things down. * Is the error reproducible on each run of mdrun? Yes * 2018.3 was not designed or tested on CUDA 10, which was released rather later. If you have an earlier CUDA, please see if building with it alleviates the error No I have only CUDA 10.0 installed. Taking into account that I made that running (see replies to the next questions) please let me know whether should I go with CUDA 9. * The error message could be triggered by multiple parts of the code; what do you get with mdrun -nb gpu -pme cpu? This way I get MD running, no crash. All 72 cores (dual Xeon Gold 6140) with my system I got $mdrun -deffnm md -v -nb gpu -pme cpu (ns/day)(hour/ns) Performance: 56.8670.422 $nvidia-smi | 0 Quadro P5000On | :D5:00.0 On | Off | | 35% 56CP063W / 180W | 1400MiB / 16256MiB | 37% Default | * Do you get any more diagnostics from running with a build with cmake -DCMAKE_BUILD_TYPE=Debug? Interesting comes here. Gromacs with Debug = ON allows to stably run MD with no additional params. I mean $ gmx mdrun -deffnm md -v runs with no crash. However, only half of the Xeon cores are used (monitored with htop) (ns/day)(hour/ns) Performance: 69.5770.345 $nvidia-smi | 0 Quadro P5000On | :D5:00.0 On | Off | | 38% 62CP068W / 180W | 1430MiB / 16256MiB | 56% Default | If I run $ gmx mdrun -deffnm md -v -nb gpu -pme cpu Then all CPU cores are busy but performancs is poor (ns/day)(hour/ns) Performance: 20.2491.185 $nvidia-smi | 0 Quadro P5000On | :D5:00.0 On | Off | | 37% 57CP058W / 180W | 1408MiB / 16256MiB | 22% Default | Finally, If I run same MD with no GPU at all (i.e. -nb cpu) then I got performance (ns/day)(hour/ns) Performance: 47.5360.505 Does this help? Dmytro From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham Sent: Wednesday, November 14, 2018 1:37 PM To: gmx-us...@gromacs.org Cc: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Running GPU issue Hi, I expect that that warning is fine (for now). The error you saw is clear evidence of a bug. There's a few things you might try to help narrow things down. * Is the error reproducible on each run of mdrun? * 2018.3 was not designed or tested on CUDA 10, which was released rather later. If you have an earlier CUDA, please see if building with it alleviates the error * The error message could be triggered by multiple parts of the code; what do you get with mdrun -nb gpu -pme cpu? * Do you get any more diagnostics from running with a build with cmake -DCMAKE_BUILD_TYPE=Debug? Mark On Wed, Nov 14, 2018 at 1:09 PM Kovalskyy, Dmytro wrote: > I forgot to add. While compiling gromacs I got following error at the very > beggining: > > > [ 3%] Built target gpu_utilstest_cuda > /usr/local/tmp/gromacs-2018.3/src/gromacs/gpu_utils/gpu_utils.cu: In > function ?int do_sanity_checks(int, cudaDeviceProp*)?: > /usr/local/tmp/gromacs-2018.3/src/gromacs/gpu_utils/gpu_utils.cu:258:28: > warning: ?cudaError_t cudaThreadSynchronize()? is deprecated > [-Wdeprecated-declarations] > if (cudaThreadSynchronize() != cudaSuccess) > ^ > /usr/local/cuda/include/cuda_runtime_api.h:947:46: note: declared here > extern __CUDA_DEPRECATED __host__ cudaError_t CUDARTAPI > cudaThreadSynchronize(void); > > > But make has completed its job without falling down. > > > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark > Abraham > Sent: Tuesday, November 13, 2018 10:29 PM > To: gmx-us...@gromacs.org > Cc: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] Running GPU issue > > Hi, > > It can share. > > Mark > > On Mon, Nov 12, 2018 at 10:19 PM Kovalskyy, Dmytro > wrote: > > > Hi, > > > > > > > > To perform GPU with Gromacs does it require exclusive GPU card or > Gromacs > > can share the video card with X-server? > > > > > > Thank you > > > > > > Dmytro > > -- > > 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/mailm
Re: [gmx-users] Running GPU issue
I forgot to add. While compiling gromacs I got following error at the very beggining: [ 3%] Built target gpu_utilstest_cuda /usr/local/tmp/gromacs-2018.3/src/gromacs/gpu_utils/gpu_utils.cu: In function ?int do_sanity_checks(int, cudaDeviceProp*)?: /usr/local/tmp/gromacs-2018.3/src/gromacs/gpu_utils/gpu_utils.cu:258:28: warning: ?cudaError_t cudaThreadSynchronize()? is deprecated [-Wdeprecated-declarations] if (cudaThreadSynchronize() != cudaSuccess) ^ /usr/local/cuda/include/cuda_runtime_api.h:947:46: note: declared here extern __CUDA_DEPRECATED __host__ cudaError_t CUDARTAPI cudaThreadSynchronize(void); But make has completed its job without falling down. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham Sent: Tuesday, November 13, 2018 10:29 PM To: gmx-us...@gromacs.org Cc: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Running GPU issue Hi, It can share. Mark On Mon, Nov 12, 2018 at 10:19 PM Kovalskyy, Dmytro wrote: > Hi, > > > > To perform GPU with Gromacs does it require exclusive GPU card or Gromacs > can share the video card with X-server? > > > Thank you > > > Dmytro > -- > 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] Running GPU issue
sigma= 0 y: E0 = 0 omega= 0 t0 = 0 sigma= 0 z: E0 = 0 omega= 0 t0 = 0 sigma= 0 grpopts: nrdf: 16011.7 141396 ref-t: 300 300 tau-t: 0.1 0.1 annealing: No No annealing-npoints: 0 0 acc:0 0 0 nfreeze: N N N energygrp-flags[ 0]: 0 Changing nstlist from 20 to 80, rlist from 0.931 to 1.049 Using 1 MPI thread Using 36 OpenMP threads 1 GPU auto-selected for this run. Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node: PP:0,PME:0 Application clocks (GPU clocks) for Quadro P5000 are (4513,1733) Application clocks (GPU clocks) for Quadro P5000 are (4513,1733) Pinning threads with an auto-selected logical core stride of 2 System total charge: -0.000 Will do PME sum in reciprocal space for electrostatic interactions. PLEASE READ AND CITE THE FOLLOWING REFERENCE U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen A smooth particle mesh Ewald method J. Chem. Phys. 103 (1995) pp. 8577-8592 --- Thank You --- Using a Gaussian width (1/beta) of 0.288146 nm for Ewald Potential shift: LJ r^-12: -3.541e+00 r^-6: -1.882e+00, Ewald -1.111e-05 Initialized non-bonded Ewald correction tables, spacing: 8.85e-04 size: 1018 Long Range LJ corr.: 3.3851e-04 Generated table with 1024 data points for Ewald. Tabscale = 500 points/nm Generated table with 1024 data points for LJ6. Tabscale = 500 points/nm Generated table with 1024 data points for LJ12. Tabscale = 500 points/nm Generated table with 1024 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1024 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1024 data points for 1-4 LJ12. Tabscale = 500 points/nm Using GPU 8x8 nonbonded short-range kernels Using a dual 8x4 pair-list setup updated with dynamic, rolling pruning: outer list: updated every 80 steps, buffer 0.149 nm, rlist 1.049 nm inner list: updated every 10 steps, buffer 0.003 nm, rlist 0.903 nm At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be: outer list: updated every 80 steps, buffer 0.292 nm, rlist 1.192 nm inner list: updated every 10 steps, buffer 0.043 nm, rlist 0.943 nm Using Lorentz-Berthelot Lennard-Jones combination rule Initializing LINear Constraint Solver PLEASE READ AND CITE THE FOLLOWING REFERENCE B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije LINCS: A Linear Constraint Solver for molecular simulations J. Comp. Chem. 18 (1997) pp. 1463-1472 --- Thank You --- The number of constraints is 8054 PLEASE READ AND CITE THE FOLLOWING REFERENCE S. Miyamoto and P. A. Kollman SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models J. Comp. Chem. 13 (1992) pp. 952-962 --- Thank You --- Intra-simulation communication will occur every 20 steps. Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest PLEASE READ AND CITE THE FOLLOWING REFERENCE G. Bussi, D. Donadio and M. Parrinello Canonical sampling through velocity rescaling J. Chem. Phys. 126 (2007) pp. 014101 --- Thank You --- There are: 78646 Atoms Started mdrun on rank 0 Tue Nov 13 16:16:25 2018 Step Time 00.0 --- Program: gmx mdrun, version 2018.3 Source file: src/gromacs/gpu_utils/cudautils.cu (line 110) Fatal error: HtoD cudaMemcpyAsync failed: invalid argument For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Thank you, Dmytro From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham Sent: Tuesday, November 13, 2018 10:29 PM To: gmx-us...@gromacs.org Cc: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Running GPU issue Hi, It can share. Mark On Mon, Nov 12, 2018 at 10:19 PM Kovalskyy, Dmytro wrote: > Hi, > > > > To perform GPU with Gromacs does it require exclusive GPU card or Gromacs > can share the video card with X-server? > > > Thank you > > > Dmytro > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting!
[gmx-users] Running GPU issue
Hi, To perform GPU with Gromacs does it require exclusive GPU card or Gromacs can share the video card with X-server? Thank you Dmytro -- 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.
