Re: [gmx-users] Turning off electrostatic between molecules
One idea, you could set the charges to zero and then build a tabulated potential to selectively mimic the electrostatic interactions between the gases and the crystal lattice. I am not sure I would call that particularly realistic, but it would be one way to selectively "turn-off" the electrostatics between different pairs. -Micholas === Micholas Dean Smith, PhD. MRSC Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Tam, Benjamin Sent: Monday, August 12, 2019 7:38:51 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [EXTERNAL] [gmx-users] Turning off electrostatic between molecules Dear All, I am thinking of a way to simulate a porous system where the gases are very diluted. I would like to add more molecules into the system in order to increase the statistic but would like to turn off molecules - molecules electrostatic interaction. I understand there are ways to turn off the Lennard Jones through [Non-bonded param] but how do you do it with charges? I still would like the gas molecules to interact with the surrounding crystal structure. Thank you very much. Best regards, Ben -- 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] Turning off electrostatic between molecules
Dear All, I am thinking of a way to simulate a porous system where the gases are very diluted. I would like to add more molecules into the system in order to increase the statistic but would like to turn off molecules - molecules electrostatic interaction. I understand there are ways to turn off the Lennard Jones through [Non-bonded param] but how do you do it with charges? I still would like the gas molecules to interact with the surrounding crystal structure. Thank you very much. Best regards, Ben -- 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] best performance on GPU
Hi, You can get significantly better performance if you use a more recent GROMACS version (>=2018) to pick up the improvements to GPU acceleration (see https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.26011 Fig 7, top group of bars), but 300 ns/day on a single machine is unlikely with your system and settings. Cheers, -- Szilárd On Fri, Aug 2, 2019 at 12:05 AM Maryam wrote: > > Dear all > I want to run a simulation of approximately 12000 atoms system in gromacs > 2016.6 on GPU with the following machine structure: > Precision: single Memory model: 64 bit MPI library: thread_mpi OpenMP > support: enabled (GMX_OPENMP_MAX_THREADS = 32) GPU support: CUDA SIMD > instructions: AVX2_256 FFT library: > fftw-3.3.5-fma-sse2-avx-avx2-avx2_128-avx512 RDTSCP usage: enabled TNG > support: enabled Hwloc support: disabled Tracing support: disabled Built > on: Fri Jun 21 09:58:11 EDT 2019 Built by: julian@BioServer [CMAKE] Build > OS/arch: Linux 4.15.0-52-generic x86_64 Build CPU vendor: AMD Build CPU > brand: AMD Ryzen 7 1800X Eight-Core Processor Build CPU family: 23 Model: 1 > Stepping: 1 > Number of GPUs detected: 1 #0: NVIDIA GeForce RTX 2080 Ti, compute cap.: > 7.5, ECC: no, stat: compatible > i used different commands to get the best performance and i dont know which > point i am missing. the quickest time possible is got by this command:gmx > mdrun -s md.tpr -nb gpu -deffnm MD -tunepme -v > which is 10 ns/day! and it takes 2 months to end. > though i used several commands to tune it like: gmx mdrun -ntomp 6 -pin on > -resethway -nstlist 20 -s md.tpr -deffnm md -cpi md.cpt -tunepme -cpt 15 > -append -gpu_id 0 -nb auto. In the gromacs website it is mentioned that > with this properties I should be able to run it in 295 ns/day! > could you help me find out what point i am missing that i can not reach the > best performance level? > Thank you > -- > -- > 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] Is it possible to control GPU utilizations when running two simulations in one workstation?
Hi, I recommend that you use fewer MPI ranks and offload PME too manually (e.g. 4 ranks 3 PP one PME) -- see the manual and recent conversations on the list related to this topic. Depending on your system size consider launching two runs side-by-side. Cheers -- Szilárd On Sat, Aug 3, 2019 at 11:11 AM sunyeping wrote: > > Dear all, > > I am trying to run a two MD simulations on one workstation equipped with 4 > GPU. First I started a simulation with the following command: > > gmx mdrun -v -deffnm md -ntmpi 12 -gpu_id 0,1 > > By the nvidia-smi command I find the utilizations of GPU 0 and 1 are 74 and > 80%, respectively. Then I started another simulation with: > > gmx mdrun -v -deffnm md -ntmpi 12 -gpu_id 2,3 > > then the utilizations of GPU 0 and 1 decreased to 20% and 23%, and the > utilizations of GPU 2 and 3, which ran the second simulation, are 12 and 15%. > Both of the two simulations ran with unbearable low speed. > > I feel it very stange because a few days ago I also ran two simulations on > the same workstation with the same mdrun commands, but the utilizations of > all four GPU were higer than 70%. Do you know what may affect the GPU > utilizations and how to correct it? > > Best regards. > -- > 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.
