Re: [gmx-users] using_gromacs_with_openmpi
Hi, Asking are you done yet? and assembling the message while it is coming off the network is work for a CPU... CPU utilization (e.g. as seen by htop utility) is necessary for maximal productivity, but it isn't sensitive about whether the work being done is useful. Mark On Wed, Apr 22, 2015 at 11:02 PM, Hossein H haji...@gmail.com wrote: But I wonder if the the performance degrade due to network latency why mdrun process uses 100% CPU on each node!!! On Thu, Apr 23, 2015 at 1:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 4/22/15 4:24 PM, Hossein H wrote: the performance degrades even when I only use two nodes!!! and the mdrun process uses almost 100% of CPU on each node Like I said, any benefit you might theoretically get from multiple CPU is being undermined by latency in the gigabit ethernet connection. It's generally not adequate for high-performance MD simulations. -Justin On Thu, Apr 23, 2015 at 12:47 AM, Justin Lemkul jalem...@vt.edu wrote: On 4/22/15 4:14 PM, Hossein H wrote: isn't gigabyte Ethernet adequate even for 2 nodes? Well, what does your benchmarking show you? Likely the performance degrades because the interconnect is simply too slow to benefit from additional CPU horsepower. -Justin On Thu, Apr 23, 2015 at 12:36 AM, Justin Lemkul jalem...@vt.edu wrote: On 4/22/15 3:59 PM, Hossein H wrote: Dear GROMACS users and developers I've compiled GROMACS 4.5.5 with gcc and *enable-mpi* option for a small cluster e.g 4 nodes on 1GbE network The code was compiled without problem and i can use it in sequential and parallel mode (using mpirun command), but the performance over the network is very poor. indeed i can run the jobs on one nodes faster than 4 nodes. because each nodes has 4 cores, i run jobs over network using following command: mpirun -np 16 --host node01,node02,node03,node04 mdrun -deffnm input -v Someone has any idea why the performance is so poor? Because you're using gigabit ethernet as your connection. That's not adequate for parallelization across machines. -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. -- == 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. -- 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
Re: [gmx-users] Optimal GPU setup for workstation with Gromacs 5
Hi JJ, On 24 Apr 2015, at 03:02, Jingjie Yeo (IHPC) ye...@ihpc.a-star.edu.sg wrote: Hi Carsten, In this case of 2 x GTX980, as far as I can tell, the clock speed and GPU ram is significantly lower. For simulations of more The GTX 980s have a clock rate of about 1200 MHz, whereas the clock rate of the Tesla K40 is 732 MHz. The latter has more CUDA cores, however. A rough estimate on how well the GROMACS short-ranged kernels perform on a card is the product of clock rate and CUDA cores. In this metric, the GTX 980 is slightly better than the K40. In addition, the GTX 980 also has the newer Maxwell generation chip, yielding somewhat higher performance due to better instruction scheduling. The amount of GPU memory is almost never an issue with GROMACS unless you want to run enormously large MD systems. The largest system that we benchmarked had 12 million atoms and this was using 1.2 GB of GPU memory, so you could even run a couple of these on a 980. In our tests with a 2 million atom system on a node with 2x E5-2680v2 processors, using two 980s resulted in a 14% increased GROMACS performance when compared to using two K40s. Note that from the money you save by buying GTX instead of Tesla cards you can get another node to run another simulation on :) Carsten than a million atoms, would it be advisable to go for more cores or more clock speed, or having both is the best case scenario? JJ -Original Message- Date: Thu, 23 Apr 2015 08:03:46 + From: Kutzner, Carsten ckut...@gwdg.de To: gmx-us...@gromacs.org gmx-us...@gromacs.org Subject: Re: [gmx-users] Optimal GPU setup for workstation with Gromacs 5 Message-ID: fe42569f-159b-49b1-a644-86a866aaa...@mpibpc.mpg.de Content-Type: text/plain; charset=us-ascii Hi, On 23 Apr 2015, at 08:03, Jingjie Yeo (IHPC) ye...@ihpc.a-star.edu.sg wrote: Dear all, My workstation specs are 2 x Intel Xeon E5-2695v2 2.40 GHz, 12 Cores. I would like to combine this with an optimal GPU setup for Gromacs 5 running simulations with millions of atoms. May I know what are the recommended setups? My vendor proposed doing a dual K40 Tesla GPU setup, would that be optimal? I would propose to put two GTX 980 into that machine instead. This will give you the same GROMACS performance at a fraction of the price. Carsten Best Regards, JJ -- 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. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] Optimal GPU setup for workstation with Gromacs 5
Hi Carsten, Thank you so much for the information! I checked with my vendor on his opinions on the GTX and his reply was that GTX cards will not minimize calculation errors the way Tesla and Quadro cards will. Do you think this is an issue? JJ -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 Kutzner, Carsten Sent: Friday, 24 April, 2015 16:40 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Optimal GPU setup for workstation with Gromacs 5 Hi JJ, On 24 Apr 2015, at 03:02, Jingjie Yeo (IHPC) ye...@ihpc.a-star.edu.sg wrote: Hi Carsten, In this case of 2 x GTX980, as far as I can tell, the clock speed and GPU ram is significantly lower. For simulations of more The GTX 980s have a clock rate of about 1200 MHz, whereas the clock rate of the Tesla K40 is 732 MHz. The latter has more CUDA cores, however. A rough estimate on how well the GROMACS short-ranged kernels perform on a card is the product of clock rate and CUDA cores. In this metric, the GTX 980 is slightly better than the K40. In addition, the GTX 980 also has the newer Maxwell generation chip, yielding somewhat higher performance due to better instruction scheduling. The amount of GPU memory is almost never an issue with GROMACS unless you want to run enormously large MD systems. The largest system that we benchmarked had 12 million atoms and this was using 1.2 GB of GPU memory, so you could even run a couple of these on a 980. In our tests with a 2 million atom system on a node with 2x E5-2680v2 processors, using two 980s resulted in a 14% increased GROMACS performance when compared to using two K40s. Note that from the money you save by buying GTX instead of Tesla cards you can get another node to run another simulation on :) Carsten than a million atoms, would it be advisable to go for more cores or more clock speed, or having both is the best case scenario? JJ -Original Message- Date: Thu, 23 Apr 2015 08:03:46 + From: Kutzner, Carsten ckut...@gwdg.de To: gmx-us...@gromacs.org gmx-us...@gromacs.org Subject: Re: [gmx-users] Optimal GPU setup for workstation with Gromacs 5 Message-ID: fe42569f-159b-49b1-a644-86a866aaa...@mpibpc.mpg.de Content-Type: text/plain; charset=us-ascii Hi, On 23 Apr 2015, at 08:03, Jingjie Yeo (IHPC) ye...@ihpc.a-star.edu.sg wrote: Dear all, My workstation specs are 2 x Intel Xeon E5-2695v2 2.40 GHz, 12 Cores. I would like to combine this with an optimal GPU setup for Gromacs 5 running simulations with millions of atoms. May I know what are the recommended setups? My vendor proposed doing a dual K40 Tesla GPU setup, would that be optimal? I would propose to put two GTX 980 into that machine instead. This will give you the same GROMACS performance at a fraction of the price. Carsten Best Regards, JJ -- 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. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] assign disulfide bond
Hi all gmx user, I want to ask if there is the way to specialized the residue index to assign a disulfide bond between 2 apart Cysteins. Because my protein is homology model so initial structure, 2 residues are apart each other. as the result, when I run pdb2gmx command, this disulfide bond can not be formed. (there is formed disulfide bond between 2 this Cysteins in wild type protein). I also took a look on specbond.dat but there no residue index is specialized. There is only the description about the residue names and atom names. CYS SG 1 CYS SG 1 0.2 CYS2CYS2 Could anybody help me? Thank you so much. Hongtham -- 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] on the regression tests
On Thu, Apr 23, 2015 at 6:29 AM, Brett brettliu...@163.com wrote: Dear All, When I install gromacs-5.0.3, after the make check step, it indicates Regression tests have not been run. If you want to run them from the build systems,get the correct version of the regression tests ackage and set REGRESSION_PATH in CMake to point to it, or set REGRESSIONTEST_DOWNLOAF=ON. Without doing the regression tests, I complete the sudo make install and source /usr/local/gromacs/bin/GMXPC steps and completing the gromacs installation. Will you please let me know is any side-effect on my gromacs installation without the regression tests? None, except that you can have lower confidence that GROMACS will work as intended. Problems are fairly unlikely, however (depending how weird your distro and compiler are). Mark -- 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] on regreressiontests
Hi, Yes, this is confusing. You can ignore the advice to check mdp differences. Mark On Fri, Apr 24, 2015 at 7:51 AM, Brett brettliu...@163.com wrote: Dear All, For my installed gromacs, I just run the regression tests. It indicates PASSED but check mdp file differences, All 12 rotation tests PASSED, All o extra tests PASSED, All 42 pdb2gmx tests PASSED. Will you please advise whether I can use my installed gromacs without concern? What does it mean for PASSED but check mdp file differences? I am looking forward to getting your reply. Brett -- 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 5.0.4 Installation error
Hi, This can't happen with a correct toolchain and unmodified source files. I think you should unpack the tarball fresh and try again. Mark On Wed, Apr 22, 2015 at 2:46 PM, Sarath Kumar Baskaran bskumar.t...@gmail.com wrote: Hi all, While Trying to install GROMACS 5.0.4 with the following compiling arguments, during make i am getting the following error, I dont know how to solve it Please help me *# cmake .. -DGMX_THREAD_MPI=ON -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-5.0.4-gpu -DGMX_GPU=ON -DGMX_BUILD_OWN_FFTW=ON -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=-5.0.4-gpu -DGMX_LIBS_SUFFIX=-5.0.4-gpu -DGMX_PREFER_STATIC_LIBS=ON -DBUILD_SHARED_LIBS=OFF* -- The C compiler identification is GNU 4.8.3 -- The CXX compiler identification is GNU 4.8.3 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Looking for NVIDIA GPUs present in the system -- Number of NVIDIA GPUs detected: 1 -- Found CUDA: /usr/local/cuda (found suitable version 7.0, minimum required is 4.0) -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detecting best SIMD instructions for this CPU -- Detected best SIMD instructions for this CPU - SSE4.1 -- Try OpenMP C flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Try OpenMP CXX flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Found OpenMP: -fopenmp -- Performing Test CFLAGS_WARN -- Performing Test CFLAGS_WARN - Success -- Performing Test CFLAGS_WARN_EXTRA -- Performing Test CFLAGS_WARN_EXTRA - Success -- Performing Test CFLAGS_WARN_REL -- Performing Test CFLAGS_WARN_REL - Success -- Performing Test CFLAGS_WARN_UNINIT -- Performing Test CFLAGS_WARN_UNINIT - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN -- Performing Test CXXFLAGS_WARN - Success -- Performing Test CXXFLAGS_WARN_EXTRA -- Performing Test CXXFLAGS_WARN_EXTRA - Success -- Performing Test CXXFLAGS_WARN_REL -- Performing Test CXXFLAGS_WARN_REL - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file regex.h -- Looking for include file regex.h - found -- Looking for C++ include regex -- Looking for C++ include regex - not found -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - found -- Looking for _aligned_malloc -- Looking for _aligned_malloc - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for rsqrt -- Looking for rsqrt - not found -- Looking for rsqrtf -- Looking for rsqrtf - not found -- Looking for sqrtf -- Looking for sqrtf - not found -- Looking for sqrt in m -- Looking for sqrt in m - found -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Using
Re: [gmx-users] Regarding Topolbuild1_3
Date: Fri, 24 Apr 2015 07:10:00 + From: Deepali Sharma deepa...@dut.ac.za To: gromacs.org_gmx-users@maillist.sys.kth.se gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Regarding Topolbuild1_3 Message-ID: 629112cec39ae346bc1195c8c8f90c9da4b51...@smlsmbx01.dut.ac.za Content-Type: text/plain; charset=UTF-8 Hi, I installed topolbuild1_3, ran the following command: /Desktop/np/topolbuild1_3/src$ ./topolbuild -dir /home/deepali/Desktop/np/topolbuild1_3/src -ff oplsaa -n ZnO -charge Fatal error. Source code file: atom_types.c, line: 87 Cannot open file /home/deepali/Desktop/np/topolbuild1_3/src/ATOMTYPE_OPLSAA1.DEF Unable to find the origin of the error. Deepali Sharma Postdoctoral Fellow Department of Chemistry Durban University of Technology (DUT) Durban, SA The error message means that the directory in which the definition files for the force fields are found is not the directory you give with the -dir specification. Judging from the directory that you gave, those files are probably located in /home/deepali/Desktop/np/topolbuild1_3/dat I hope that helps. -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St., Rm. LD-061 Indianapolis, IN 46202 -- 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_simd_check_and_reset_overflow undefined for sparc64 hpc ace
Hi all, I'm having trouble compiling gromacs (from git master) for sparc64 SIMD. It fails with gromacs/src/gromacs/mdlib/tpi.cpp, line 470: error: identifier gmx_simd_check_and_reset_overflow is undefined gmx_simd_check_and_reset_overflow(); It looks like this should be defined in simd/impl_sparc64_hpc_ace.h but isn't. Has anyone run into this? I noticed that for some of the SIMD implementations (intel qpx, vmx, vsx), that function just returns 0. Is that appropriate here? Thanks, Matt -- 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] membrane protein simulation
Hi Tsjerk, Yes, it would be very helpful. thanks for your help. Best regards, Mostafa On Thu, Apr 23, 2015 at 9:40 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Mostafa, We have a complete simulation system of bacteriorhodopsin in the purple membrane, which you can use as basis for your simulations if you want. Best, Tsjerk On Apr 22, 2015 10:08 PM, Mostafa Javaheri javaheri.grom...@gmail.com wrote: Dear Justin I am going to simulate a homo trimer trans-membrane protein; Base on the crystallographic structures there is 7 phosphatidyl glycerol phosphate (PGP) per each monomer and also 3 glycolipid molecules (S-TGA-1, or 3-HSO 3 -Galpβ1-6ManpR1-2GlcpR-1-archeol) located inside the trimer on the extracellular side of membrane. In the membrane protein tutorial of gromacs 1,2-dipalmitoyl-*sn*-glycero-3-phosphatidylcholine (DPPC) is introduced as the standard lipids, so should I treat PGPs and glycolipids as ligands and going through protein ligand complex tutorial? Or treat glycolipids as ligands, continue the membrane protein tutorial and use DPPCs instead of PGPs? Is it OK if I replace PGP with DPPC from the standpoint of simulation? Sincerely -- 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] Optimal GPU setup for workstation with Gromacs 5
Hi Carsten, Thank you so much for the information! Seems like the GTX is the way to go. One last question, regarding the Maxwell architecture, would there be any kind of backward compatibility issue, say if I need to use both Gromacs 4.6 and 5.0, since it is the newest architecture? JJ -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 Kutzner, Carsten Sent: Friday, April 24, 2015 5:51 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Optimal GPU setup for workstation with Gromacs 5 Hi JJ, On 24 Apr 2015, at 10:53, Jingjie Yeo (IHPC) ye...@ihpc.a-star.edu.sg wrote: Hi Carsten, Thank you so much for the information! I checked with my vendor on his opinions on the GTX and his reply was that GTX cards will not minimize calculation errors the way Tesla and Quadro cards will. Do you think this is an issue? The GeForce cards do not offer ECC memory, so they cannot pick up memory errors occurring on the GPU, which are however very unlikely. Run an extensive memory check (e.g. memtestCL) before first usage of the cards. We have tested nearly 300 GeForce cards, and only 7 of them had problems with memory, so we replaced them. Carsten JJ -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 Kutzner, Carsten Sent: Friday, 24 April, 2015 16:40 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Optimal GPU setup for workstation with Gromacs 5 Hi JJ, On 24 Apr 2015, at 03:02, Jingjie Yeo (IHPC) ye...@ihpc.a-star.edu.sg wrote: Hi Carsten, In this case of 2 x GTX980, as far as I can tell, the clock speed and GPU ram is significantly lower. For simulations of more The GTX 980s have a clock rate of about 1200 MHz, whereas the clock rate of the Tesla K40 is 732 MHz. The latter has more CUDA cores, however. A rough estimate on how well the GROMACS short-ranged kernels perform on a card is the product of clock rate and CUDA cores. In this metric, the GTX 980 is slightly better than the K40. In addition, the GTX 980 also has the newer Maxwell generation chip, yielding somewhat higher performance due to better instruction scheduling. The amount of GPU memory is almost never an issue with GROMACS unless you want to run enormously large MD systems. The largest system that we benchmarked had 12 million atoms and this was using 1.2 GB of GPU memory, so you could even run a couple of these on a 980. In our tests with a 2 million atom system on a node with 2x E5-2680v2 processors, using two 980s resulted in a 14% increased GROMACS performance when compared to using two K40s. Note that from the money you save by buying GTX instead of Tesla cards you can get another node to run another simulation on :) Carsten than a million atoms, would it be advisable to go for more cores or more clock speed, or having both is the best case scenario? JJ -Original Message- Date: Thu, 23 Apr 2015 08:03:46 + From: Kutzner, Carsten ckut...@gwdg.de To: gmx-us...@gromacs.org gmx-us...@gromacs.org Subject: Re: [gmx-users] Optimal GPU setup for workstation with Gromacs 5 Message-ID: fe42569f-159b-49b1-a644-86a866aaa...@mpibpc.mpg.de Content-Type: text/plain; charset=us-ascii Hi, On 23 Apr 2015, at 08:03, Jingjie Yeo (IHPC) ye...@ihpc.a-star.edu.sg wrote: Dear all, My workstation specs are 2 x Intel Xeon E5-2695v2 2.40 GHz, 12 Cores. I would like to combine this with an optimal GPU setup for Gromacs 5 running simulations with millions of atoms. May I know what are the recommended setups? My vendor proposed doing a dual K40 Tesla GPU setup, would that be optimal? I would propose to put two GTX 980 into that machine instead. This will give you the same GROMACS performance at a fraction of the price. Carsten Best Regards, JJ -- 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. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner
[gmx-users] pdb2gmx and periodic molecule
Ahoy, What I have here is a 100% precisely set up periodic ssdna chain of six residues without termini. The goal is to get the 'polymerization' across the box. So, I boxed the chain and set up the periodicity pretty much perfectly. To test, translation in the direction of periodicity by the periodicity constant results in bonds perfectly recognized by things like VMD or pymol (in the concatenated structure). When running pdb2gmx on the boxed structure, the periodicity seems to be ignored and then expectedly I get a fatal error with a custom FF that works fine on finite chains. x2top sees pbc, but we're not using it here. So, no topology in sight. Any ideas? Thanks, Alex p.s. I can post the test structure if there's any doubt about periodicity of the structure itself. -- 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] About Analsysi tool
Dear Justin Thank you for your previous reply, I am doing Dynamics for CNT-wraapped by Cyclic peptide . The Cyclic peptide i am stacking Beyond Hydrogen bond distance. AT end of Simulation, the Assembly become Collapsed Is there is Any tool To list out interaction energy and analyze the interaction energy (may be decomposing during simulation) between Cyclic peptides and Between Cyclic peptides Vs CNT Thanks in Advance S.Vidhyasankar -- 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] help on Graphene Nano Sheets
Hi people, I was able to run the graphene layer sheet, by follow your advices. I had a problem with the dihetral angle, i solved it by chancing, im the top file the funct parameter from 1 to 3, as reported in bold below, . [ dihedrals ] ; aiajakal functc0c1 c2 c3c4c5 6 1 2 3 *3 * 2 1 6 5 *3 * 2 18887 *3* 1 2 3 4 *3 * ... and also, by changing in rtp files all_dihedrals from 1 to 0, .. [ bondedtypes ] ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih 1 1 3 1 *0* 3 1 0 .. But, when i run the mdrun file, after the minimizzation, the model result destroyer, all the atom of graphene are spreads arround monitor, and they are not yet connected as in the original geometry. I would like to have some advices. What is wrong? how i have to set the dihedral angles? Thanks. Il 23/04/2015 20:04, abhijit Kayal ha scritto: Hi Mercelo Copy the oplsaa.ff directory to your working directory. Then in ffnonbonded.itp file add the following lines.. opls_995 C 612.01100 0.000 A3.4e-01 3.61200e-01 opls_996 C 612.01100 0.000 A3.4e-01 3.61200e-01 opls_997 C 612.01100 0.000 A3.4e-01 3.61200e-01 Then in atomname2type.n2t file add the following lines. Copls_9950 12.011 2C 0.142 C 0.142 Copls_9960 12.011 3C 0.142 C 0.142 C 0.142 Copls_9970 12.011 1C 0.142 Then use g_x2top. This will work. On Thu, Apr 23, 2015 at 10:54 PM, Alex nedoma...@gmail.com wrote: I think we've covered this when I was having the same issue. If you're trying to simulate a multi-molecule system, then just copy the entire forcefield .ff folder to your local directory and modify the following files: ffbonded.itp ffnonbonded.itp atomnames2types.n2t No need to create rtp entries for graphene/nanotubes, so you can ignore that part of Andrea's tutorial. Instead of just C in his tutorial, come up with a unique label to avoid conflicts, which should then also be used in your PDB. Then what I would do is create a topology entry for just graphene and convert it to a stand-alone itp by stripping off system definitions. This is basically opening the top file, removing those definitions and resaving as *.itp. After that, you can just use pdb2gmx on the remaining parts of the system and complete the system topology by hand. I know, this sounds like a lot of manual tweaking, but this is the paradigm. Good luck! Alex MC I run a graphene nanolayer, usin the below description (from previous mail. MC Now i got an other error. It look like there is a conflict in a force MC field system, someone can suggest me how to modify it? MC the force field file came from Minoia advices, reported in the web side! MC / MC //Program grompp, VERSION 4.6.7// MC //Source code file: MC /home/marcello/DATI/software/gromacs-4.6.7/src/kernel/topio.c, line: 752// MC // MC //Fatal error:// MC //Syntax error - File forcefield.itp, line 31// MC //Last line read:// MC //'1 3 yes 0.5 0.5'// MC //Found a second defaults directive./* MC * -- 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. -- Marcello Cammarata, Ph.D. 3208790796 -- 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] help on Graphene Nano Sheets
Andrea Minoia's tutorial describes the setup of angles, which in the case of graphene, is extremely simple from the geometry standpoint. There is no need for chancing, just add the proper entries under [dihedraltypes] in ffbonded.itp, x2top will take care of the rest. It's also a pretty good idea to actually read the manual on the definition of angles and dihedrals. Energy minimization destroys the sheet, because there's a mess in your setup. Alex MC Hi people, MC I was able to run the graphene layer sheet, by follow your advices. MC I had a problem with the dihetral angle, MC i solved it by chancing, im the top file the funct parameter from 1 to MC 3, as reported in bold below, MC . MC [ dihedrals ] MC ; aiajakal functc0c1 c2 MC c3c4c5 MC 6 1 2 3 *3 * MC 2 1 6 5 *3 * MC 2 18887 *3* MC 1 2 3 4 *3 * MC ... MC and also, by changing in rtp files all_dihedrals from 1 to 0, MC .. MC [ bondedtypes ] MC ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih MC 1 1 3 1 *0* 3 1 0 MC .. MC But, when i run the mdrun file, after the minimizzation, the model MC result destroyer, all the atom of graphene are spreads arround monitor, MC and they are not yet connected as in the original geometry. MC I would like to have some advices. What is wrong? how i have to set the MC dihedral angles? MC Thanks. MC Il 23/04/2015 20:04, abhijit Kayal ha scritto: Hi Mercelo Copy the oplsaa.ff directory to your working directory. Then in ffnonbonded.itp file add the following lines.. opls_995 C 612.01100 0.000 A3.4e-01 3.61200e-01 opls_996 C 612.01100 0.000 A3.4e-01 3.61200e-01 opls_997 C 612.01100 0.000 A3.4e-01 3.61200e-01 Then in atomname2type.n2t file add the following lines. Copls_9950 12.011 2C 0.142 C 0.142 Copls_9960 12.011 3C 0.142 C 0.142 C 0.142 Copls_9970 12.011 1C 0.142 Then use g_x2top. This will work. On Thu, Apr 23, 2015 at 10:54 PM, Alex nedoma...@gmail.com wrote: I think we've covered this when I was having the same issue. If you're trying to simulate a multi-molecule system, then just copy the entire forcefield .ff folder to your local directory and modify the following files: ffbonded.itp ffnonbonded.itp atomnames2types.n2t No need to create rtp entries for graphene/nanotubes, so you can ignore that part of Andrea's tutorial. Instead of just C in his tutorial, come up with a unique label to avoid conflicts, which should then also be used in your PDB. Then what I would do is create a topology entry for just graphene and convert it to a stand-alone itp by stripping off system definitions. This is basically opening the top file, removing those definitions and resaving as *.itp. After that, you can just use pdb2gmx on the remaining parts of the system and complete the system topology by hand. I know, this sounds like a lot of manual tweaking, but this is the paradigm. Good luck! Alex MC I run a graphene nanolayer, usin the below description (from previous mail. MC Now i got an other error. It look like there is a conflict in a force MC field system, someone can suggest me how to modify it? MC the force field file came from Minoia advices, reported in the web side! MC / MC //Program grompp, VERSION 4.6.7// MC //Source code file: MC /home/marcello/DATI/software/gromacs-4.6.7/src/kernel/topio.c, line: 752// MC // MC //Fatal error:// MC //Syntax error - File forcefield.itp, line 31// MC //Last line read:// MC //'1 3 yes 0.5 0.5'// MC //Found a second defaults directive./* MC * -- 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. MC -- MC Marcello Cammarata, Ph.D. MC 3208790796 -- 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.org_gmx-users Digest, Vol 132, Issue 117
Hi I am trying to launch a simulation of ameloblastin (421 amino acids). This will take long time. But can you help me to estimate how much time I must put as wall time on the script below? I used 500hours, it run then the simulation stopped after that time, when I increased at 1700hours, then the simulation never start!!! I have 68 000CPU hours remain on my account. Please advise. Thanks. SCRIPT: #!/bin/bash #PBS -lnodes=2:ppn=16 #PBS -lwalltime=500:00:00 #PSB -lpmem=5500MB workdir=/global/work/$USER/$PBS_JOBID mkdir -p $workdir cd $PBS_O_WORKDIR cp md.mdp nvt.gro nvt.cpt topol.top $workdir cd $workdir module load gromacs/4.5.5 grompp -f md.mdp -c nvt.gro -t nvt.cpt -p topol.top -o md_0_1.tpr -maxwarn 10 -zero mdrun -deffnm md_0_1 -nt 8 echo Info from the system echo PDW ls -la $PWD echo Workdir ls -la $workdir echo DIR ls -la echo PBS_O_WORKDIR ls -la $PBS_O_WORKDIR echo Start copy data ... cp * $PBS_O_WORKDIR echo Check your data and do not forget remove $workdir #rm -rf $workdir Simon -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 132, Issue 117
Please use a real subject line rather than generically replying to the digest. On 4/24/15 1:32 PM, Simon Longela wrote: Hi I am trying to launch a simulation of ameloblastin (421 amino acids). This will take long time. But can you help me to estimate how much time I must put as wall time on the script below? Run a short benchmark. Even a few thousand steps would be enough. I used 500hours, it run then the simulation stopped after that time, when I This is what checkpointing is for. It doesn't matter if the job stops because of a wallclock limit, mdrun -cpi will pick up from where it left off. -Justin increased at 1700hours, then the simulation never start!!! I have 68 000CPU hours remain on my account. Please advise. Thanks. SCRIPT: #!/bin/bash #PBS -lnodes=2:ppn=16 #PBS -lwalltime=500:00:00 #PSB -lpmem=5500MB workdir=/global/work/$USER/$PBS_JOBID mkdir -p $workdir cd $PBS_O_WORKDIR cp md.mdp nvt.gro nvt.cpt topol.top $workdir cd $workdir module load gromacs/4.5.5 grompp -f md.mdp -c nvt.gro -t nvt.cpt -p topol.top -o md_0_1.tpr -maxwarn 10 -zero mdrun -deffnm md_0_1 -nt 8 echo Info from the system echo PDW ls -la $PWD echo Workdir ls -la $workdir echo DIR ls -la echo PBS_O_WORKDIR ls -la $PBS_O_WORKDIR echo Start copy data ... cp * $PBS_O_WORKDIR echo Check your data and do not forget remove $workdir #rm -rf $workdir Simon -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Regarding Topolbuild1_3
Hi, I installed topolbuild1_3, ran the following command: /Desktop/np/topolbuild1_3/src$ ./topolbuild -dir /home/deepali/Desktop/np/topolbuild1_3/src -ff oplsaa -n ZnO -charge Fatal error. Source code file: atom_types.c, line: 87 Cannot open file /home/deepali/Desktop/np/topolbuild1_3/src/ATOMTYPE_OPLSAA1.DEF Unable to find the origin of the error. Deepali Sharma Postdoctoral Fellow Department of Chemistry Durban University of Technology (DUT) Durban, SA This e-mail is subject to our Disclaimer, to view click http://www.dut.ac.za/disclaimer; Disclaimer The information contained in this communication from the sender is confidential. It is intended solely for use by the recipient and others authorized to receive it. If you are not the recipient, you are hereby notified that any disclosure, copying, distribution or taking action in relation of the contents of this information is strictly prohibited and may be unlawful. This email has been scanned for viruses and malware, and automatically archived by Mimecast SA (Pty) Ltd, an innovator in Software as a Service (SaaS) for business. Mimecast Unified Email Management (UEM) offers email continuity, security, archiving and compliance with all current legislation. To find out more, visit http://www.mimecast.co.za/uem. -- 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] Command-Line Options for Cray XK7 Nodes
Hi all, How can I find the command line options used for the benchmarks at the end of the http://www.gromacs.org/GPU_acceleration; page? I'm running a similarly-sized simulation (200k atoms) on Titan, which is also XK7/K20X. After many attempts that did not run at all (I'm new to Gromacs), I've settled on this so far, using 64 nodes, which gets me 57.581 ns/day: aprun -n 512 -S 4 -j 1 -d 1 mdrun_mpi -v -dlb yes -gpu_id 00 -npme 128 For reference: Each node has a 16-core Bulldozer processor and an nVidia GPU. The processor is structured as shown here: https://www.olcf.ornl.gov/kb_articles/xk7-cpu-description/ Thank you for your help! Mitchell Dorrell -- 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.
