Re: [gmx-users] gromacs binaries for windows (Cygwin 64)
Sorry I wrote the previous mail without revise. Thank you for your comments. As in message in the cmake configure process, gcc on 64 bit windows is buggy for AVX simd instruction. 1. I cannot use -DGMX_BUILD_OWN_FFTW=ON. I used FFTW on Cygwin repo. 2. With AVX I could Gromacs 2018 or later but binary are broken. With SSE simd instruction, Gromacs works all versions Usable binary with AVX can be build on Gromacs 2016 or before. Please also see Notes for Cygwin build (http://tmacchant3.starfree.jp/gromacs/win/notes_cygwin.html) on my web site. Now I added MSVC binary (http://tmacchant3.starfree.jp/gromacs/win) and Notes for MSVC build (http://tmacchant3.starfree.jp/gromacs/win/notes_MSVC.html). Tatsuro - Original Message - > From: Tatsuro MATSUOKA > To: Szilárd Páll ; Discussion list for GROMACS users > > Cc: "gromacs.org_gmx-users@maillist.sys.kth.se" > > Date: 2019/9/11, Wed 11:54 > Subject: Re: [gmx-users] gromacs binaries for windows (Cygwin 64) > >T hank you for your comments. > As in cmake configure process, gcc on 64 bit windows is buggy for AVX simd > instruction. > > > 1. I cannot use -DGMX_BUILD_OWN_FFTW=ON. I used FFTW on Cygwin repo. > 2. With AVX I could Gromacs 2018 or later but binary are broken before. > Usable binary can be Gromacs 2016 or before. > > Please also SEE Notes on my web site. > > Now I adde MSVC binary. > > > Tatsuro > > > > > - Original Message - >> From: Szilárd Páll >> To: Discussion list for GROMACS users ; > Tatsuro MATSUOKA >> Cc: "gromacs.org_gmx-users@maillist.sys.kth.se" > >> Date: 2019/9/10, Tue 18:21 >> Subject: Re: [gmx-users] gromacs binaries for windows (Cygwin 64) >> >> Dear Tatsuro, >> >> Thanks for the contributions! >> >> Do the builds work out cleanly on cygwin? Are there any additional >> instructions we should consider including in our installation guide? >> >> Cheers, >> -- >> Szilárd >> >> On Fri, Sep 6, 2019 at 5:46 AM Tatsuro MATSUOKA > >> wrote: >>> >>> I have prepared gromacs binaries for windows (Cygwin 64) on my own web > >> site. >>> (For testing purpose.) >>> >>> http://tmacchant3.starfree.jp/gromacs/win/ >>> >>> Tatsuro >>> >>> -- >>> 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] gromacs binaries for windows (Cygwin 64)
Thank you for your comments. As in cmake configure process, gcc on 64 bit windows is buggy for AVX simd instruction. 1. I cannot use -DGMX_BUILD_OWN_FFTW=ON. I used FFTW on Cygwin repo. 2. With AVX I could Gromacs 2018 or later but binary are broken before. Usable binary can be Gromacs 2016 or before. Please also SEE Notes on my web site. Now I adde MSVC binary. Tatsuro - Original Message - > From: Szilárd Páll > To: Discussion list for GROMACS users ; Tatsuro > MATSUOKA > Cc: "gromacs.org_gmx-users@maillist.sys.kth.se" > > Date: 2019/9/10, Tue 18:21 > Subject: Re: [gmx-users] gromacs binaries for windows (Cygwin 64) > > Dear Tatsuro, > > Thanks for the contributions! > > Do the builds work out cleanly on cygwin? Are there any additional > instructions we should consider including in our installation guide? > > Cheers, > -- > Szilárd > > On Fri, Sep 6, 2019 at 5:46 AM Tatsuro MATSUOKA > wrote: >> >> I have prepared gromacs binaries for windows (Cygwin 64) on my own web > site. >> (For testing purpose.) >> >> http://tmacchant3.starfree.jp/gromacs/win/ >> >> Tatsuro >> >> -- >> 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] gromacs binaries for windows (Cygwin 64)
Thanks for comments. > I'm curious: is there any advantage of using Cygwin over using WSL > (https://docs.microsoft.com/en-us/windows/wsl/install-win10 ) for using > GROMACS? > If you use WSL than installing GROMACS on Windows is trivial. First "Notes for Cygwin build" I mentioned WSL build as : On Windows 10 64bit, one of the efficient method to build GROMACS is to use the WSL (Windows Subsystem for Linux). Information of setting up the WSL and building steps of GROMACS on the WSL can be found by search engines (e. g. Google). Building GROMACS on Cygwin is sometimes useful because binaries can be portable. I now added MSVC compiled binaries not using icc. At this moment I can only use AVX but not AVX2, AVX512. Tatsuro - Original Message - > From: "Schulz, Roland" > To: "gmx-us...@gromacs.org" ; Tatsuro MATSUOKA > > Cc: "gromacs.org_gmx-users@maillist.sys.kth.se" > > Date: 2019/9/11, Wed 02:49 > Subject: RE: [gmx-users] gromacs binaries for windows (Cygwin 64) > > I'm curious: is there any advantage of using Cygwin over using WSL > (https://docs.microsoft.com/en-us/windows/wsl/install-win10 ) for using > GROMACS? > If you use WSL than installing GROMACS on Windows is trivial. > > MSVC has also AVX512 support: > https://devblogs.microsoft.com/cppblog/microsoft-visual-studio-2017-supports-intel-avx-512/ > > > https://github.com/MicrosoftDocs/cpp-docs/issues/1078 > > I haven't tested whether AVX2 or AVX512 works correctly with MSVC. > > Also note that it's possible to produce native Windows binaries (without a > dependency on Cygwin/Mingw/WSL) compiled for AVX2 and AVX512 with LLVM and > ICC: > https://github.com/boostorg/hana/wiki/Setting-up-Clang-on-Windows#visual-studio-2015-with-clangllvm-clang-cl > > > https://software.intel.com/en-us/system-studio/choose-download > > Roland > >> -Original Message- >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se >> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of >> Szilárd Páll >> Sent: Tuesday, September 10, 2019 2:21 AM >> To: Discussion list for GROMACS users ; > Tatsuro >> MATSUOKA >> Cc: gromacs.org_gmx-users@maillist.sys.kth.se >> Subject: Re: [gmx-users] gromacs binaries for windows (Cygwin 64) >> >> Dear Tatsuro, >> >> Thanks for the contributions! >> >> Do the builds work out cleanly on cygwin? Are there any additional >> instructions we should consider including in our installation guide? >> >> Cheers, >> -- >> Szilárd >> >> On Fri, Sep 6, 2019 at 5:46 AM Tatsuro MATSUOKA >> wrote: >> > >> > I have prepared gromacs binaries for windows (Cygwin 64) on my own web >> site. >> > (For testing purpose.) >> > >> > http://tmacchant3.starfree.jp/gromacs/win/ >> > >> > Tatsuro >> > >> > -- >> > 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] How to use gmx h2order when using four point water model
Hi all, I want to obtain the water dipole orientation at the interface using gmx h2order. It works well when I I use 3 point water model, like SPC/E. The manual says that the order of water should be O H H, but for 4 point water model, there is a vitual atom, and this command cannot output the correct results. Is there any solutions for this poblem? Thanks, Jun -- 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] MSVC or later now supports AVX2 and AVX_512
Sorry I have make mistake. Check for AVX2 was passed by modification. * In CmakeCache.txt C_arch_AVX2_COMPILE_WORKS:INTERNAL=1 //Test C_arch_AVX2_FLAG_ACCEPTED * But actually simd/impl_x86_avx_256 codes were built but not simd/impl_x86_avx2_256. Tatsuro - Original Message - >From: Mark Abraham >To: Discussion list for GROMACS users ; Tatsuro >MATSUOKA >Cc: "gromacs.org_gmx-users@maillist.sys.kth.se" > >Date: 2019/9/10, Tue 18:17 >Subject: Re: [gmx-users] MSVC or later now supports AVX2 and AVX_512 > > >Hi, > > >Thanks for the report. Do the tests pass? Particularly the simd-test binary. > > >Mark > >On Tue, 10 Sep 2019 at 09:36, Tatsuro MATSUOKA wrote: > >In gmxSimdFlags.cmake, it is described : >># no AVX2-specific flag for MSVC yet >> >>However, at least MSVC 2017 and 2019, /arch:AVX2 is added. >>If I modify /arch:AVX to /arch:AVX2, gromacs can be complied with avx 256. >> >>Tatsuro >> >>-- >>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] Tyrosine to phosphotyrosine conversion a must in phosphorylation protein ?
Dear Seke Yes it Is obligatory to phosphorylate the tyrosine. Use 43a1p extended phosphorylated force field you will get good results after comparing both non phosphorylated and phosphorylated structures Regards Najam On Wed, Sep 4, 2019 at 7:31 AM Seketoulie Keretsu wrote: > Dear expert, > > This is not a gromacs problem however I'm wondering if you can give some > insight and direction to go look further. > > I have a protein phosphorylation protein kinase with a phosphotyrosine at a > position 20 angstrom away from the binding site. I want to perform an MD to > study the protein ligand interaction and binding energy calculations. I > wonder if the modeling of the tyrosine to phophotyrosine is imperative for > such studies. Is there any review or study done comparing such changes? I > know newer force fields supports phosphorylation residues but wanted to > know if failing to use phosphorylation structure would make the study > useless. > > Your inputs will be appreciated. > > Thank you. > > Sincerely, > > Seke > -- > 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] gromacs binaries for windows (Cygwin 64)
PS: When it comes to installing a FFT library to compile a native binary, in my experience the two easiest choices are: - If you anyhow use ICC then to use MKL instead of FFTW not requiring any extra steps - Otherwise use the FFTW3 port from vcpkg. Just make sure to enable AVX/AVX2 Roland > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of > Schulz, Roland > Sent: Tuesday, September 10, 2019 10:49 AM > To: gmx-us...@gromacs.org; Tatsuro MATSUOKA > Cc: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] gromacs binaries for windows (Cygwin 64) > > I'm curious: is there any advantage of using Cygwin over using WSL > (https://docs.microsoft.com/en-us/windows/wsl/install-win10) for using > GROMACS? > If you use WSL than installing GROMACS on Windows is trivial. > > MSVC has also AVX512 support: > https://devblogs.microsoft.com/cppblog/microsoft-visual-studio-2017- > supports-intel-avx-512/ > https://github.com/MicrosoftDocs/cpp-docs/issues/1078 > > I haven't tested whether AVX2 or AVX512 works correctly with MSVC. > > Also note that it's possible to produce native Windows binaries (without a > dependency on Cygwin/Mingw/WSL) compiled for AVX2 and AVX512 with > LLVM and ICC: > https://github.com/boostorg/hana/wiki/Setting-up-Clang-on- > Windows#visual-studio-2015-with-clangllvm-clang-cl > https://software.intel.com/en-us/system-studio/choose-download > > Roland > > > -Original Message- > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > > [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf > > Of Szilárd Páll > > Sent: Tuesday, September 10, 2019 2:21 AM > > To: Discussion list for GROMACS users ; Tatsuro > > MATSUOKA > > Cc: gromacs.org_gmx-users@maillist.sys.kth.se > > Subject: Re: [gmx-users] gromacs binaries for windows (Cygwin 64) > > > > Dear Tatsuro, > > > > Thanks for the contributions! > > > > Do the builds work out cleanly on cygwin? Are there any additional > > instructions we should consider including in our installation guide? > > > > Cheers, > > -- > > Szilárd > > > > On Fri, Sep 6, 2019 at 5:46 AM Tatsuro MATSUOKA > > wrote: > > > > > > I have prepared gromacs binaries for windows (Cygwin 64) on my own > > > web > > site. > > > (For testing purpose.) > > > > > > http://tmacchant3.starfree.jp/gromacs/win/ > > > > > > Tatsuro > > > > > > -- > > > 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.
Re: [gmx-users] gromacs binaries for windows (Cygwin 64)
I'm curious: is there any advantage of using Cygwin over using WSL (https://docs.microsoft.com/en-us/windows/wsl/install-win10) for using GROMACS? If you use WSL than installing GROMACS on Windows is trivial. MSVC has also AVX512 support: https://devblogs.microsoft.com/cppblog/microsoft-visual-studio-2017-supports-intel-avx-512/ https://github.com/MicrosoftDocs/cpp-docs/issues/1078 I haven't tested whether AVX2 or AVX512 works correctly with MSVC. Also note that it's possible to produce native Windows binaries (without a dependency on Cygwin/Mingw/WSL) compiled for AVX2 and AVX512 with LLVM and ICC: https://github.com/boostorg/hana/wiki/Setting-up-Clang-on-Windows#visual-studio-2015-with-clangllvm-clang-cl https://software.intel.com/en-us/system-studio/choose-download Roland > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of > Szilárd Páll > Sent: Tuesday, September 10, 2019 2:21 AM > To: Discussion list for GROMACS users ; Tatsuro > MATSUOKA > Cc: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] gromacs binaries for windows (Cygwin 64) > > Dear Tatsuro, > > Thanks for the contributions! > > Do the builds work out cleanly on cygwin? Are there any additional > instructions we should consider including in our installation guide? > > Cheers, > -- > Szilárd > > On Fri, Sep 6, 2019 at 5:46 AM Tatsuro MATSUOKA > wrote: > > > > I have prepared gromacs binaries for windows (Cygwin 64) on my own web > site. > > (For testing purpose.) > > > > http://tmacchant3.starfree.jp/gromacs/win/ > > > > Tatsuro > > > > -- > > 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] gmx pairdist help
Hi all, I'm trying calculate the pairwise distance between each of my protein residues and my ligand molecules. I type the following command: gmx pairdist -f Traj.xtc -s Traj.tpr -n mindist.ndx -selrpos whole_res_com -refgrouping res -o dist.xvg -type min When I don't type the "-selrpos whole_res_com" I get the same values so by default is it working out from the COM of each individual residue? Akash -- 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] grompp not possible with annealing - Gromacs 2019.1
Hi, Thanks for the report - but it's probably fixed already ( http://manual.gromacs.org/documentation/2019.2/release-notes/2019/2019.2.html#fix-segmentation-fault-when-preparing-simulated-annealing-inputs) so I suggest you get the latest 2019.x release? Mark On Tue, 10 Sep 2019 at 17:15, Tafelmeier, Stefanie < stefanie.tafelme...@zae-bayern.de> wrote: > Dear all, > > I try to use simulation annealing, but unfortunately the grompp - command > leads to an error. > It is not a known Gromacs error, but it doesn't finish the job and it > says: Speicherzugriffsfehler (Speicherabzug geschrieben) (which means > something like "Memory Access Error") > > The only output file produced is the mdout.mdp, which content seems > correct. > > The screen text is given below as well as the grompp.mdp content and the > details to the system used. > > There have been some issues as well to get Gromacs installed on the > workstation. Not sure if this could be connected. > Many thanks already for your help. > > Greetings, > Steffi > > > > > Screen text: > > GROMACS: gmx grompp, version 2019.1 > Executable: /usr/local/gromacs/bin/gmx > Data prefix: /usr/local/gromacs > Working dir: > /home/pcm-mess/Schreibtisch/StTa/Vergleich_FF/OPLS/fixed_layer/freeze_grp/temp_grps/annealing > Command line: > gmx grompp -f grompp_OPLS_anneal.mdp -v > > checking input for internal consistency... > Setting the LD random seed to -28800458 > processing topology... > Generated 330891 of the 330891 non-bonded parameter combinations > Generating 1-4 interactions: fudge = 0.5 > Generated 330891 of the 330891 1-4 parameter combinations > Excluding 3 bonded neighbours molecule type 'Other' > turning all bonds into constraints... > > NOTE 1 [file unknown]: > You are using constraints on all bonds, whereas the forcefield has been > parametrized only with constraints involving hydrogen atoms. We suggest > using constraints = h-bonds instead, this will also improve performance. > > processing coordinates... > double-checking input for internal consistency... > Setting gen_seed to -1070611718 > Velocities were taken from a Maxwell distribution at 280 K > Removing all charge groups because cutoff-scheme=Verlet > renumbering atomtypes... > converting bonded parameters... > initialising group options... > processing index file... > Analysing residue names: > There are: 3600 Other residues > Analysing residues not classified as Protein/DNA/RNA/Water and splitting > into groups... > Speicherzugriffsfehler (Speicherabzug geschrieben) > > > > > > Content grompp.mdp (as an example): > > include = -I../top > define = > cutoff-scheme= Verlet > integrator = md > dt = 0.001 > nsteps = 80 > nstxout = 2000 > nstvout = 2000 > nstlog = 2000 > nstenergy= 2000 > nstlist = 10 > ns-type = grid > pbc = xyz > rlist= 1 > coulombtype = PME > rcoulomb = 1 > rvdw = 1 > tcoupl = v-rescale > tc-grps = other > tau-t= 0.1 > ref-t= 280 > Pcoupl = Berendsen > pcoupltype = anisotropic > tau-p= 10 > compressibility = 8.7e-5 8.7e-5 8.7e-5 0 0 0 > ref-p= 1.0 1.0 1.0 0 0 0 > constraints = all-bonds > gen-vel = yes > gen-temp = 280 > gen-seed = -1 > annealing = single > annealing-npoints = 2 > annealing-time = 0 60 > annealing-temp = 280 280 > > > > > > System details: > > GROMACS version:2019.1 > Precision: single > Memory model: 64 bit > MPI library:thread_mpi > OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 128) > GPU support:CUDA > SIMD instructions: AVX_512 > FFT library:fftw-3.3.8-sse2-avx-avx2-avx2_128-avx512 > RDTSCP usage: enabled > TNG support:enabled > Hwloc support: disabled > Tracing support:disabled > C compiler: /usr/bin/cc GNU 8.2.0 > C compiler flags:-mavx512f -mfma -O3 -DNDEBUG -funroll-all-loops > -fexcess-precision=fast > C++ compiler: /usr/bin/c++ GNU 8.2.0 > C++ compiler flags: -mavx512f -mfma-std=c++11 -O3 -DNDEBUG >
[gmx-users] grompp not possible with annealing - Gromacs 2019.1
Dear all, I try to use simulation annealing, but unfortunately the grompp - command leads to an error. It is not a known Gromacs error, but it doesn't finish the job and it says: Speicherzugriffsfehler (Speicherabzug geschrieben) (which means something like "Memory Access Error") The only output file produced is the mdout.mdp, which content seems correct. The screen text is given below as well as the grompp.mdp content and the details to the system used. There have been some issues as well to get Gromacs installed on the workstation. Not sure if this could be connected. Many thanks already for your help. Greetings, Steffi Screen text: GROMACS: gmx grompp, version 2019.1 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /home/pcm-mess/Schreibtisch/StTa/Vergleich_FF/OPLS/fixed_layer/freeze_grp/temp_grps/annealing Command line: gmx grompp -f grompp_OPLS_anneal.mdp -v checking input for internal consistency... Setting the LD random seed to -28800458 processing topology... Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Other' turning all bonds into constraints... NOTE 1 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. processing coordinates... double-checking input for internal consistency... Setting gen_seed to -1070611718 Velocities were taken from a Maxwell distribution at 280 K Removing all charge groups because cutoff-scheme=Verlet renumbering atomtypes... converting bonded parameters... initialising group options... processing index file... Analysing residue names: There are: 3600 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Speicherzugriffsfehler (Speicherabzug geschrieben) Content grompp.mdp (as an example): include = -I../top define = cutoff-scheme= Verlet integrator = md dt = 0.001 nsteps = 80 nstxout = 2000 nstvout = 2000 nstlog = 2000 nstenergy= 2000 nstlist = 10 ns-type = grid pbc = xyz rlist= 1 coulombtype = PME rcoulomb = 1 rvdw = 1 tcoupl = v-rescale tc-grps = other tau-t= 0.1 ref-t= 280 Pcoupl = Berendsen pcoupltype = anisotropic tau-p= 10 compressibility = 8.7e-5 8.7e-5 8.7e-5 0 0 0 ref-p= 1.0 1.0 1.0 0 0 0 constraints = all-bonds gen-vel = yes gen-temp = 280 gen-seed = -1 annealing = single annealing-npoints = 2 annealing-time = 0 60 annealing-temp = 280 280 System details: GROMACS version:2019.1 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 128) GPU support:CUDA SIMD instructions: AVX_512 FFT library:fftw-3.3.8-sse2-avx-avx2-avx2_128-avx512 RDTSCP usage: enabled TNG support:enabled Hwloc support: disabled Tracing support:disabled C compiler: /usr/bin/cc GNU 8.2.0 C compiler flags:-mavx512f -mfma -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast C++ compiler: /usr/bin/c++ GNU 8.2.0 C++ compiler flags: -mavx512f -mfma-std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast CUDA compiler: /usr/local/cuda-10.1/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2019 NVIDIA Corporation;Built on Fri_Feb__8_19:08:17_PST_2019;Cuda compilation tools, release 10.1, V10.1.105 CUDA compiler
Re: [gmx-users] gromacs binaries for windows (Cygwin 64)
Dear Tatsuro, Thanks for the contributions! Do the builds work out cleanly on cygwin? Are there any additional instructions we should consider including in our installation guide? Cheers, -- Szilárd On Fri, Sep 6, 2019 at 5:46 AM Tatsuro MATSUOKA wrote: > > I have prepared gromacs binaries for windows (Cygwin 64) on my own web site. > (For testing purpose.) > > http://tmacchant3.starfree.jp/gromacs/win/ > > Tatsuro > > -- > 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] MSVC or later now supports AVX2 and AVX_512
Hi, Thanks for the report. Do the tests pass? Particularly the simd-test binary. Mark On Tue, 10 Sep 2019 at 09:36, Tatsuro MATSUOKA wrote: > In gmxSimdFlags.cmake, it is described : > # no AVX2-specific flag for MSVC yet > > However, at least MSVC 2017 and 2019, /arch:AVX2 is added. > If I modify /arch:AVX to /arch:AVX2, gromacs can be complied with avx 256. > > Tatsuro > > -- > 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] DSSP graph re-scale
Dear Syah, the answer depends on the way you're creating .eps file. I'm assuming that you're using the gmx do_dssp then gmx xpm2ps. something like this can be used: gmx do_dssp -f final.xtc -s my.tpr -n new.ndx -map first.map -tu ns -b 700 -e 1000 -o protein.xpm gmx xpm2ps -f protein.xpm -di scale.m2p -title top -bx 8.0 -by 50 -o sec_struc_new.eps if the x-axis ticks is the problem, you can change the font or anything related to it, in the .m2p file. ( http://manual.gromacs.org/archive/5.0.3/online/m2p.html) I hope you find it useful. Best regards, Mohammadreza Niknam Hamidabad On Tue, Sep 10, 2019 at 6:18 AM SGR160055 Student wrote: > Dear experts, > > I have an issue to re-scale the x-axis on DSSP graph eps format for my 100 > ns simulation time. > > The x-axis of the graph became too compact until it can't be read clearly. > > How should I solve this? Is there anyway to re-scale the graph for eps > format. > > Your help is much appreciated. Thank you. > > > > Regards, > Syah > -- > 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] MSVC or later now supports AVX2 and AVX_512
In gmxSimdFlags.cmake, it is described : # no AVX2-specific flag for MSVC yet However, at least MSVC 2017 and 2019, /arch:AVX2 is added. If I modify /arch:AVX to /arch:AVX2, gromacs can be complied with avx 256. Tatsuro -- 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] mdrun error
Hi gromacs user I am simulating protein ionic liquid(IL) system, in my IL forcefield the function type of dihedral parameter is 5. When I am running gmx mdrun it appears the following error. Program: gmx mdrun, version 2018.1 Source file: src/gromacs/topology/topsort.cpp (line 139) Fatal error: Function type Fourier Dih. not implemented in ip_pert For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor After getting this error I have used function type 3 that also showed Ryckaert-Bellemans dihedral error Any suggestion will be appreciated to resolve this problem. ** *Krishna Prasad GhantaResearch Scholar* *Molecular Modeling Laboratory* *Indian Institute Of Technology Kharagpur* *Kharagpur-721302Contact no - 8327297650* *** -- 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.
