[gmx-users] modeling of zwitter-ions
Hello, I'm simulating a molecule which is aminoacid connected with drug throuch a "bridge" of a few C-C bonds. Molecule should be in zwitter-ionic form, where negative and positive charges are distributed in pi-systems of drug and amino-acid, accordingly. Which is the best way to build the topology of such zwitter-ion? And one more question. The solvent is acetonitrile and it's important to take into account the solvation effects in this system. I'm working in gromos54a7 forcefield. Which acenotitrile model is better for solvatation effects? -- Best regards, Olga Selyutina -- 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] Workstation choice
Hi, Mirco. 2018-09-11 3:29 GMT+07:00 Wahab Mirco : > > How would the 8600K perform without GPU (using the "-nb cpu" > option on the mdrun binary)? > > 8600K with frequency 4600Mhz was used Command line: gmx mdrun -nb cpu Core t (s) Wall t (s)(%) Time: 1529.942 254.990 600.0 (ns/day)(hour/ns) Performance: 169.4190.142 Finished mdrun on rank 0 Wed Sep 12 02:29:41 2018 It may be interesting, the run with only 3 threads: Command line: gmx mdrun -nb cpu -nt 3 Core t (s) Wall t (s)(%) Time: 1435.090 478.363 300.0 (ns/day)(hour/ns) Performance: 90.3080.266 Finished mdrun on rank 0 Wed Sep 12 02:44:50 2018 - a single R2-2700X possibly cannot always saturate TWO > GTX-1080/1080Ti (maybe Szilárd Páll can add some rule of > thumb whether and when it can), > >- due to AVX2_512, 6C/12T "Coffee Lake" i7 may be somehow faster than > even 8C/16T Ryzen2 (at some scenarios significantly?) > Thank you, it's very helpful information. > I can provide some performance numbers I got after updating > Gromacs to v.2018.3 lately on our aging lab hardware. > > ==> (I can provide the input file if required) ==> Yes, it will be great if you can provide some test results with input file (maybe it can help) -- Best regards, Olga Selyutina -- 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] Workstation choice
Hi, Páll 2018-09-11 21:50 GMT+07:00 Szilárd Páll : > I've presonally not tried the 2nd-gen Ryzen, but based on the performance > of the 1800X and the compute benchmarks I've seen published, these will > likely be the best value for money (possibly the 2600X if that allows > getting better GPUs?). > It makes sence. Benchmarks are very similar but price is about 30% lower! I'll think carefully about it. > Special edition CPU, not worth the money unless you like the name ;) > > It's for lovers of rare names :) > Don't forget that you need a few other components too in particular note > that that the motherboard will be more expensive for Threadripper, cheaper > for Ryzen 7 (and unless Intel boards are also a bit more pricey than the > Ryzens). > > Yes, I remember. The cost of other components was taken into account when choosing CPU and GPU. 2018-09-11 21:55 GMT+07:00 Szilárd Páll : > > Also, I can't (yet) recommend AMD GPUs as a buying option for > consumer-grade stuff as we don't yet have PME offload support in OpenCL, > but this will soon change. > > Thanks for advice, I haven't take AMD GPUs into account yet. > > Glad to hear. Feel free to follow up if you have further questions (but do > allow some time for replies ;). > > Thank you, I will :) -- Best regards, Olga Selyutina -- 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] Workstation choice
> > > (50 ts instead of 5000 ts, otherwise it's too fast) > > > That would be a factor of about 227! On an available machine (not used for simulations) self-compiled 2018.3, CUDA 9.1 the similar result, factor is about 136: Working dir: /home/user/dev/gromacs/gmxbench-3.0/d.poly-ch2 Command line: gmx mdrun -ntmpi 1 -nt 6 Running on 1 node with total 6 cores, 6 logical cores, 1 compatible GPU Hardware detected: CPU info: Vendor: Intel Brand: Intel(R) Core(TM) i5-8600K CPU @ 3.60GHz GPU info: Number of GPUs detected: 1 #0: NVIDIA GeForce GTX 1050 Ti, compute cap.: 6.1, ECC: no, stat: compatible On 1 MPI rank, each using 6 OpenMP threads Core t (s) Wall t (s)(%) Time: 1102.853183.809 600.0 (ns/day)(hour/ns) Performance: 235.0270.102 Finished mdrun on rank 0 Tue Sep 11 01:53:36 2018 -- Best regards, Olga Selyutina -- 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] Workstation choice
Thank you, an idea to build own low-price cluster is very interesting. Seven Ryzen 3 2200 with hardware cost ~$2000 and their total performance for some purposes could be higher than performance of one high-performance CPU with few GPUs (configurations CPU+GPUs mentioned in my previous letter) . But I’m not sure that they provide higher performance for GROMACS simulations. 2018-09-09 12:59 GMT+07:00 Benson Muite : > This is old, but seems to indicate Beowulf clusters work quite well: > > https://docs.uabgrid.uab.edu/wiki/Gromacs_Benchmark > > Szilárd had helped create a benchmark data set available at: > http://www.gromacs.org/About_Gromacs/Benchmarks > http://www.gromacs.org/@api/deki/files/240/=gromacs-5.0-benchmarks.pdf > ftp://ftp.gromacs.org/pub/benchmarks/gmxbench-3.0.tar.gz > > Does your use case involves a large number of ensemble simulations which > can be done in single precision without error correction? If so might you > be better building a small Beowulf cluster with lower spec processors that > have integrated GPUs? For example a Ryzen 3 with integrated graphics is > about $100. Motherboard, RAM, power supply would probably get you to about > $300. Intel core I3 bundle would be about $350. Setup could be done using > OpenHPC stack: > http://www.openhpc.community/ > > This would get you a personal 5-7 node in house cluster. However, ability > to do maintenance, have local support for repair may also be important in > considering system lifetime cost, not just initial purchase price. Gromacs > current and future support for OpenCl, and likely also important here. > > At least one computer store in my region has allowed benchmarking. > > On 09/07/2018 09:40 PM, Olga Selyutina wrote: > >> Hi, >> A lot of thanks for valuable information. >> If it isn’t difficult for you, could you answer how the growth of >> performance under using the second GPU on the single simulation was >> changed >> in GROMACS 2018 vs older versions (2016, 5.1, it was 20-30% higher)? >> >> >> 2018-09-07 23:25 GMT+07:00 Szilárd Páll : >> >> Are you intending to use it mostly/only for running simulations or also as >>> a desktop computer? >>> >>> Yes, it will be mostly used for simulations. >>> >> >> I'm not on the top of pricing details so you should probably look at some >>> configs and get back with concrete CPU + GPU (+price) combinations and we >>> might be able to guesstimate what's best. >>> >>> >>> These sets of CPU and GPU are suitable for price (in our region): >> *GPU* >> GTX 1070 ~1700MHz, cuda 1920 - $514 >> GTX 1080 ~1700MHz, cuda 2560 - $615 >> GTX 1070Ti ~1700MHz, cuda 2432 - $615 >> GTX 1080Ti ~1600MHz, cuda 3584 - $930 >> >> *CPU* >> Ryzen 7 2700X - $357 >> 4200MHz, 8/16 cores/threads, cache L1/L2/L3 768KB/4MB/16MB, 105W, max.T >> 85C >> >> Threadripper 1950X - $930 >> 4000MHz, 16/32 cores/threads, cache L1/L2/L3 1.5/8/32MB, 180W, max.T 68C >> >> i7 8086K - $515 >> 4800MHz, 6/12 cores/threads, cache L2/L3 1.5/12MB, 95W, max.T 100C >> >> i7 8700K - $442 >> 4600MHz, 6/12 cores/threads, cache L2/L3 1.5/12MB, 95W, max.T 100C >> >> The most suitable combinations CPU+GPU are as follows: >> 1) Ryzen 7 2700X + two GTX 1080 - $1587 >> 1.1) Ryzen 7 2700X + one GTX 1080 + one GTX 1080*Ti* - $1900 (maybe?) >> 2) Threadripper 1950X + one GTX 1080Ti - $1860 >> 3) i7 8700K + two GTX 1080 - $1672 >> 4) Ryzen 7 2700X + three GTX 1070 - $1900 >> My suggestions: >> Variant 1 seems to be the most suitable. >> Variant 2 seems to be suitable only if the single simulation is running on >> workstation >> It’s a bit confusing that in synthetic tests/games performance of i7 8700 >> is higher than Ryzen 7 2700. >> Thanks a lot again for your advice, it has already clarified a lot! >> >> >> >> > -- > 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. > -- С уважением, Ольга Селютина -- 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] Workstation choice
Hi, A lot of thanks for valuable information. If it isn’t difficult for you, could you answer how the growth of performance under using the second GPU on the single simulation was changed in GROMACS 2018 vs older versions (2016, 5.1, it was 20-30% higher)? 2018-09-07 23:25 GMT+07:00 Szilárd Páll : > > Are you intending to use it mostly/only for running simulations or also as > a desktop computer? > > Yes, it will be mostly used for simulations. > I'm not on the top of pricing details so you should probably look at some > configs and get back with concrete CPU + GPU (+price) combinations and we > might be able to guesstimate what's best. > > These sets of CPU and GPU are suitable for price (in our region): *GPU* GTX 1070 ~1700MHz, cuda 1920 - $514 GTX 1080 ~1700MHz, cuda 2560 - $615 GTX 1070Ti ~1700MHz, cuda 2432 - $615 GTX 1080Ti ~1600MHz, cuda 3584 - $930 *CPU* Ryzen 7 2700X - $357 4200MHz, 8/16 cores/threads, cache L1/L2/L3 768KB/4MB/16MB, 105W, max.T 85C Threadripper 1950X - $930 4000MHz, 16/32 cores/threads, cache L1/L2/L3 1.5/8/32MB, 180W, max.T 68C i7 8086K - $515 4800MHz, 6/12 cores/threads, cache L2/L3 1.5/12MB, 95W, max.T 100C i7 8700K - $442 4600MHz, 6/12 cores/threads, cache L2/L3 1.5/12MB, 95W, max.T 100C The most suitable combinations CPU+GPU are as follows: 1) Ryzen 7 2700X + two GTX 1080 - $1587 1.1) Ryzen 7 2700X + one GTX 1080 + one GTX 1080*Ti* - $1900 (maybe?) 2) Threadripper 1950X + one GTX 1080Ti - $1860 3) i7 8700K + two GTX 1080 - $1672 4) Ryzen 7 2700X + three GTX 1070 - $1900 My suggestions: Variant 1 seems to be the most suitable. Variant 2 seems to be suitable only if the single simulation is running on workstation It’s a bit confusing that in synthetic tests/games performance of i7 8700 is higher than Ryzen 7 2700. Thanks a lot again for your advice, it has already clarified a lot! -- Best regards, Olga Selyutina -- 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] Workstation choice
Thank you, to use these tests isn’t a problem, but available workstation are too old, so test results won’t be helpful in choosing actual components. I have an access to high-performance cluster, but it also couldn’t be the basis because of its high cost. If it is hard to give the certain recommendation, I would to know at least how do performance correlate with the number of cores/threads and core frequency? What is more important the core frequency or number of cores? What is preferable, Intel or AMD? How should be correlated GPU and CPU performance? In the previous letters in mail-list I found recommendations on purchase of Threadripper 1950X+GeForce GTX-1080Ti, I think that more cheap and similar effective choice is TR 1950X+GeForce GTX-*1080*. Will there be significant differences with 1)TR 19*20*X+GeForce GTX-1080 2) Intel 7900x+GeForce GTX-1080? 2018-09-05 20:53 GMT+07:00 Benson Muite : > Hi Olga, > > The authors of: > > https://github.com/bio-phys/MDBenchmark/tree/version-1.3.2 > > https://zenodo.org/record/1318123 > > May be helpful. If your data is not confidential, you may consider running > Gromacs remotely on a cloud high performance computing resource, or > benchmarking remotely and then purchasing a suitable configuration. > > Some other information: > http://manual.gromacs.org/documentation/current/user-guide/ > mdrun-performance.html# > http://www.gromacs.org/GPU_acceleration > https://extras.csc.fi/chem/courses/gmx2007/Erik_Talks/buildi > ng_clusters.pdf > http://www.gromacs.org/Documentation/Performance_checklist > > On 09/05/2018 12:02 PM, Olga Selyutina wrote: > >> Hello, >> >> I need help in choice of the workstation for MD simulations using GROMACS. >> It is supposed to study systems consisting from 30-50k atoms, in >> particular, lipid bilayer models. Since the last generation of Intel and >> Ryzen CPU has made a big leap in performance, available workstation can’t >> be taken as a basis. Please, help to choose components of the workstation, >> particularly, GPU and CPU with total cost about $2000. What is better, to >> buy two GPUs(sli) or one GPU but more effective? >> >> > -- > 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. -- Best regards, Olga Selyutina -- 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] Workstation choice
Hello, I need help in choice of the workstation for MD simulations using GROMACS. It is supposed to study systems consisting from 30-50k atoms, in particular, lipid bilayer models. Since the last generation of Intel and Ryzen CPU has made a big leap in performance, available workstation can’t be taken as a basis. Please, help to choose components of the workstation, particularly, GPU and CPU with total cost about $2000. What is better, to buy two GPUs(sli) or one GPU but more effective? -- Best rerards, Olga Selyutina -- 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.
