[gmx-users] Failed HardwareTopologyTest on Install (GROMACS 2019.4)
Hey all,
I am trying to install GROMACS 2019.4 (patched with plumed 2.5.3) on the
Bridges <https://portal.xsede.org/psc-bridges> cluster, which uses Intel
Haswell CPUS. When compiling/installing with GNU compiler (GCC 4.8.4) and
OpenMPI, the compile runs well. The cmake command I used was :
cmake .. \
-DCMAKE_C_COMPILER=mpicc \
-DCMAKE_CXX_COMPILER=mpicxx \
-DGMX_MPI=ON \
-DCMAKE_INSTALL_PREFIX="${INSTALL_ROOT}" \
-DGMX_BUILD_OWN_FFTW=OFF \
-DGMX_FFT_LIBRARY=fftw3 \
-DREGRESSIONTEST_PATH="${BUILD_ROOT}/regressiontests-2019.4" \
-DGMX_SIMD=AVX2_256
Upon running 'make check', I pass 47/48 tests. The only test I fail is the
HardwareUnitTests, specifically the HardwareTopologyTest. The error message
I receive is reproduced below.
---
11/46 Test #11: HardwareUnitTests ...***Failed0.65 sec
[==] Running 5 tests from 2 test cases.
[--] Global test environment set-up.
[--] 1 test from CpuInfoTest
[ RUN ] CpuInfoTest.SupportLevel
[ OK ] CpuInfoTest.SupportLevel (1 ms)
[--] 1 test from CpuInfoTest (1 ms total)
[--] 4 tests from HardwareTopologyTest
[ RUN ] HardwareTopologyTest.Execute
[ OK ] HardwareTopologyTest.Execute (57 ms)
[ RUN ] HardwareTopologyTest.HwlocExecute
/pylon5/mc5fphp/anto/gromacs_src/gromacs-2019.4/src/gromacs/hardware/tests/hardwaretopology.cpp:88:
Failure
Expected: (hwTop.supportLevel()) >=
(gmx::HardwareTopology::SupportLevel::Basic), actual: 4-byte object <01-00
00-00> vs 4-byte object <02-00 00-00>
Cannot determine basic hardware topology from hwloc. GROMACS will still
work, but it might affect your performance for large nodes.
Please mail gmx-develop...@gromacs.org so we can try to fix it.
[ FAILED ] HardwareTopologyTest.HwlocExecute (51 ms)
[ RUN ] HardwareTopologyTest.ProcessorSelfconsistency
[ OK ] HardwareTopologyTest.ProcessorSelfconsistency (50 ms)
[ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency
[ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (48 ms)
[--] 4 tests from HardwareTopologyTest (206 ms total)
[--] Global test environment tear-down
[==] 5 tests from 2 test cases ran. (207 ms total)
[ PASSED ] 4 tests.
[ FAILED ] 1 test, listed below:
[ FAILED ] HardwareTopologyTest.HwlocExecute
1 FAILED TEST
.
.
.
98% tests passed, 1 tests failed out of 46
Label Time Summary:
GTest = 137.68 sec (40 tests)
IntegrationTest= 103.21 sec (5 tests)
MpiTest= 1.36 sec (3 tests)
SlowTest = 15.28 sec (1 test)
UnitTest = 19.18 sec (34 tests)
Total Test time (real) = 1461.58 sec
The following tests FAILED:
11 - HardwareUnitTests (Failed)
Errors while running CTest
make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8
make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2
make[1]: *** [CMakeFiles/check
The rest of the tests pass without issue, so . Any ideas? Is this some
issue with hwloc, and is there anything I can do to fix it, or do I need to
contact the sys admins? Is this a big issue, even with the failed test? The
nodes only ever have 24 CPUs, so I'm not sure if that counts as a 'large
node' (or if the number of nodes used per simulation would matter). Thanks
in advance for the help! By the way, I am emailing this list because the
error message told me to email gmx-developers, but I don't have permissions
to post there - I apologize if this is the wrong forum.
Thanks so much!
--
Adam Antoszewski, PhD Candidate
Dept. of Chemistry, The University of Chicago
antoszew...@uchicago.edu
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[gmx-users] short range electrostatic cutoff
Hi all, I'm trying to find a way to prevent infinite attractive forces between oppositely charged particles in my system using a purely coulombic potential (without using a LJ potential). Does gromacs provide a way to cutoff coulomb potential at short range, i.e. below a certain radius, the coulombic potential stays constant instead of decreasing to negative infinity? I can't seem to find any options that would do this. Thanks, Adam -- 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] PRACE benchmarks
Hi Mark,
Hmm. Other applications have been working with OpenMPI, but that
doesn't invalidate your point.
Is there a particular implementation you recommend for GROMACS?
Cheers,
Adam
On Thu, Jul 14, 2016 at 11:00 AM, Mark Abraham wrote:
> Hi,
>
> Looks like your MPI setup is broken. So far, I have only heard of people
> having problems when using OpenMPI 1.10.x, even the latest patch release.
>
> Mark
>
> On Thu, Jul 14, 2016 at 11:52 AM Adam Huffman
> wrote:
>
>> Hello
>>
>> I've been trying to run the PRACE benchmarks on a new cluster:
>>
>> http://www.prace-ri.eu/ueabs/#GROMACS
>>
>> and this is the command-line I've been running:
>>
>> mpirun --mca plm_base_verbose 10 --debug-daemons gmx_mpi mdrun -s
>> ion_channel.tpr -maxh 0.50 -resethway -noconfout -nsteps 1 -g
>> logfile-${SLURM_JOB_ID}
>>
>> This was running over several days, so I tried again, with 1000 steps,
>> and then even with 10 steps, but the jobs are running seemingly
>> without doing anything:
>>
>> sstat -j 1511 --format
>> Nodelist,NTasks,AveCPU,AveDiskRead,AveDiskWrite,AveRSS,AvePages
>> Nodelist NTasks AveCPU AveDiskRead AveDiskWrite
>> AveRSS AvePages
>> --
>> -- --
>> ca[127-157]0 00:00.00000
>> 0 0
>>
>> I'm certainly no expert on GROMACS so I would appreciate it if someone
>> could point out any glaring errors in that mdrun invocation. (I added
>> the MPI debug flags for separate reasons).
>>
>> The logfile shows:
>>
>> Command line:
>> gmx_mpi mdrun -v -s lignocellulose-rf.BGQ.tpr -maxh 0.50 -resethway
>> -noconfout -nsteps 10 -g logfile-B-1-1511
>>
>> GROMACS version:VERSION 5.1.2
>> Precision: single
>> Memory model: 64 bit
>> MPI library:MPI
>> OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
>> GPU support:disabled
>> OpenCL support: disabled
>> invsqrt routine:gmx_software_invsqrt(x)
>> SIMD instructions: AVX_256
>> FFT library:fftw-3.3.4-sse2
>> RDTSCP usage: enabled
>> C++11 compilation: enabled
>> TNG support:enabled
>> Tracing support:disabled
>> Built on: Thu 30 Jun 07:39:10 BST 2016
>> Built by: huff...@login000.camp.thecrick.org [CMAKE]
>> Build OS/arch: Linux 3.10.0-327.18.2.el7.x86_64 x86_64
>> Build CPU vendor: GenuineIntel
>> Build CPU brand:Intel Xeon E312xx (Sandy Bridge)
>> Build CPU family: 6 Model: 42 Stepping: 1
>> Build CPU features: aes apic avx clfsh cmov cx8 cx16 lahf_lm mmx msr
>> pclmuldq popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
>> C compiler:
>> /camp/apps/eb/software/OpenMPI/1.10.2-GCC-4.9.3-2.25/bin/mpicc GNU
>> 4.9.3
>> C compiler flags:-mavx -fopenmp -O2 -march=native -Wundef
>> -Wextra -Wno-missing-field-initializers -Wno-sign-compare
>> -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter
>> -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
>> -Wno-array-bounds
>> C++ compiler:
>> /camp/apps/eb/software/OpenMPI/1.10.2-GCC-4.9.3-2.25/bin/mpicxx GNU
>> 4.9.3
>> C++ compiler flags: -mavx -std=c++0x -fopenmp -O2 -march=native
>> -Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall
>> -Wno-unused-function -O3 -DNDEBUG -funroll-all-loops
>> -fexcess-precision=fast -Wno-array-bounds
>> Boost version: 1.60.0 (external)
>>
>> and nothing after that.
>>
>> strace of one of the processes shows:
>>
>> [pid 1374] poll([{fd=5, events=POLLIN}, {fd=12, events=POLLIN},
>> {fd=15, events=POLLIN}], 3, 0) = 0 (Timeout)
>>
>>
>> Cheers,
>> Adam
>> --
>> 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
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>
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>
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[gmx-users] PRACE benchmarks
Hello
I've been trying to run the PRACE benchmarks on a new cluster:
http://www.prace-ri.eu/ueabs/#GROMACS
and this is the command-line I've been running:
mpirun --mca plm_base_verbose 10 --debug-daemons gmx_mpi mdrun -s
ion_channel.tpr -maxh 0.50 -resethway -noconfout -nsteps 1 -g
logfile-${SLURM_JOB_ID}
This was running over several days, so I tried again, with 1000 steps,
and then even with 10 steps, but the jobs are running seemingly
without doing anything:
sstat -j 1511 --format
Nodelist,NTasks,AveCPU,AveDiskRead,AveDiskWrite,AveRSS,AvePages
Nodelist NTasks AveCPU AveDiskRead AveDiskWrite
AveRSS AvePages
--
-- --
ca[127-157]0 00:00.00000
0 0
I'm certainly no expert on GROMACS so I would appreciate it if someone
could point out any glaring errors in that mdrun invocation. (I added
the MPI debug flags for separate reasons).
The logfile shows:
Command line:
gmx_mpi mdrun -v -s lignocellulose-rf.BGQ.tpr -maxh 0.50 -resethway
-noconfout -nsteps 10 -g logfile-B-1-1511
GROMACS version:VERSION 5.1.2
Precision: single
Memory model: 64 bit
MPI library:MPI
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
GPU support:disabled
OpenCL support: disabled
invsqrt routine:gmx_software_invsqrt(x)
SIMD instructions: AVX_256
FFT library:fftw-3.3.4-sse2
RDTSCP usage: enabled
C++11 compilation: enabled
TNG support:enabled
Tracing support:disabled
Built on: Thu 30 Jun 07:39:10 BST 2016
Built by: huff...@login000.camp.thecrick.org [CMAKE]
Build OS/arch: Linux 3.10.0-327.18.2.el7.x86_64 x86_64
Build CPU vendor: GenuineIntel
Build CPU brand:Intel Xeon E312xx (Sandy Bridge)
Build CPU family: 6 Model: 42 Stepping: 1
Build CPU features: aes apic avx clfsh cmov cx8 cx16 lahf_lm mmx msr
pclmuldq popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
C compiler:
/camp/apps/eb/software/OpenMPI/1.10.2-GCC-4.9.3-2.25/bin/mpicc GNU
4.9.3
C compiler flags:-mavx -fopenmp -O2 -march=native -Wundef
-Wextra -Wno-missing-field-initializers -Wno-sign-compare
-Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter
-O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
-Wno-array-bounds
C++ compiler:
/camp/apps/eb/software/OpenMPI/1.10.2-GCC-4.9.3-2.25/bin/mpicxx GNU
4.9.3
C++ compiler flags: -mavx -std=c++0x -fopenmp -O2 -march=native
-Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall
-Wno-unused-function -O3 -DNDEBUG -funroll-all-loops
-fexcess-precision=fast -Wno-array-bounds
Boost version: 1.60.0 (external)
and nothing after that.
strace of one of the processes shows:
[pid 1374] poll([{fd=5, events=POLLIN}, {fd=12, events=POLLIN},
{fd=15, events=POLLIN}], 3, 0) = 0 (Timeout)
Cheers,
Adam
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Re: [gmx-users] Details of 5.0 benchmark report?
Hi Szilárd, Yes, it's certainly not worth a large effort to try and recover the information. Thanks for the link, which should be very useful. The next time you're looking at something like this, it might be worth trying to capture what might be useful for others to run tests themselves. Thanks again, Adam On Tue, Apr 12, 2016 at 5:36 PM, Szilárd Páll wrote: > Adam, > > The job scripts used in those benchmarks are all specific to the > machines, and while admittedly the launch configuration information > could be useful to have next to each data point, I'm afraid we don't > have such data readily extracted from the run logs, I believe. I did > not compile the document myself, but unless such data has been parsed > and it's just not presented, it would be a quite large effort to go > back and extract such information for quite little benefit (as the > exact ranks/thread configurations will change with GROMACS versions, > compilers, libraries, machine load, etc.) > > I recommend you to have a look at recent benchmark papers that contain > detailed information on what to tune and how to run parallel jobs, > e.g. > http://onlinelibrary.wiley.com/doi/10.1002/jcc.24030/full > Scaling of the GROMACS 4.6 molecular dynamics code on SuperMUC. > > Cheers, > -- > Szilárd > > > On Mon, Apr 11, 2016 at 2:00 PM, Adam Huffman wrote: >> Hello >> >> Ideal would be to have the command-lines that were used, for those of >> us that aren't GROMACS experts. >> >> Cheers, >> Adam >> >> On Tue, Mar 8, 2016 at 5:08 PM, Szilárd Páll wrote: >>> Hi, >>> >>> What details are you interested in? IIRC the inputs are clearly specified >>> (although perhaps not provided there). >>> >>> -- >>> Szilárd >>> >>> On Fri, Mar 4, 2016 at 5:15 PM, Adam Huffman wrote: >>> >>>> Hello >>>> >>>> Are details of the running of the benchmarks reported for version 5.0 >>>> available anywhere? >>>> >>>> I'm referring to the report published at: >>>> >>>> http://www.gromacs.org/@api/deki/files/240/=gromacs-5.0-benchmarks.pdf >>>> >>>> I would like to be able to run these myself, on three different systems. >>>> >>>> >>>> Cheers, >>>> Adam >>>> -- >>>> 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. -- 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] Details of 5.0 benchmark report?
Hello Ideal would be to have the command-lines that were used, for those of us that aren't GROMACS experts. Cheers, Adam On Tue, Mar 8, 2016 at 5:08 PM, Szilárd Páll wrote: > Hi, > > What details are you interested in? IIRC the inputs are clearly specified > (although perhaps not provided there). > > -- > Szilárd > > On Fri, Mar 4, 2016 at 5:15 PM, Adam Huffman wrote: > >> Hello >> >> Are details of the running of the benchmarks reported for version 5.0 >> available anywhere? >> >> I'm referring to the report published at: >> >> http://www.gromacs.org/@api/deki/files/240/=gromacs-5.0-benchmarks.pdf >> >> I would like to be able to run these myself, on three different systems. >> >> >> Cheers, >> Adam >> -- >> 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] Details of 5.0 benchmark report?
Hello Are details of the running of the benchmarks reported for version 5.0 available anywhere? I'm referring to the report published at: http://www.gromacs.org/@api/deki/files/240/=gromacs-5.0-benchmarks.pdf I would like to be able to run these myself, on three different systems. Cheers, Adam -- 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] ADD_LIBRARY cmake error on Bluegene/Q
Just to follow up on this, upgrading cmake from 2.8.8 (to 3.13 in this case) solved the problem. Adam From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Irina Kosheleva Sent: 12 February 2016 15:18 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] ADD_LIBRARY cmake error on Bluegene/Q Hello Adam For me alcf scientist suggested to compile with: Use xl compilers in your .soft environment. cmake -DCMAKE_C_COMPILER=mpixlc_r -DCMAKE_CXX_COMPILER=mpixlcxx_r -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C -DGMX_SIMD=IBM_QPX -DFFTWF_INCLUDE_DIR=/soft/libraries/alcf/current/xl/FFTW3/include -DFFTWF_LIBRARY=/soft/libraries/alcf/current/xl/FFTW3/lib/libfftw3f.a -DBUILD_SHARED_LIBS=OFF -DGMX_XML=OFF -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_C_FLAGS="-O3 -qsmp=omp -qarch=qp -qtune=qp" -DCMAKE_INSTALL_PREFIX= It does not work for me because I have trouble compiling libxml2 library - suspect that come from Gromacs cmake command parsing- but if you do not care - it may work for you. Irina. -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 Hardy, Adam Sent: Friday, February 12, 2016 5:44 AM To: gmx-us...@gromacs.org Subject: [gmx-users] ADD_LIBRARY cmake error on Bluegene/Q Dear all, I'm having some difficulty compiling GROMACS 5.1.1 on a Bluegene/Q machine. This is using the xl compiler. I recieve the error: ADD_LIBRARY for library mdrun_objlib is used with the MODULE option, but the target platform supports only STATIC libraries. Building it STATIC instead. This may lead to problems. -- Configuring done CMake Error at src/programs/CMakeLists.txt:45 (add_executable): Objects of target "mdrun_objlib" referenced but is not an OBJECT library. If I attempt to compile it, it fails: Linking CXX executable ../../bin/mdrun_mpi_d CMakeFiles/mdrun.dir/mdrun_main.cpp.o:(.toc+0x0): undefined reference to `gmx_mdrun(int, char**)' My cmake command is as follow: export CMAKE_PREFIX_PATH=/cineca/prod/libraries/fftw/3.3.3/bgq-xl--1.0/lib/ export FLAGS="-O3 -qarch=qp -qtune=qp" export FFTW_INC_DIR=/cineca/prod/libraries/fftw/3.3.3/bgq-xl--1.0/include/ export INSTALL_PRE=/fermi/home/userexternal/hbock000/gmx/ cmake ../ -DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_GPU=OFF -DGMX_X11=OFF -DGMX_DOUBLE=ON \ -DCMAKE_C_FLAGS="$FLAGS" -DCMAKE_CXX_FLAGS="$FLAGS" -DGMX_BUILD_MDRUN_ONLY=ON \ -DFFTW_INCLUDE_DIR=$FFTW_INC_DIR \ -DCMAKE_INSTALL_PREFIX=$INSTALL_PRE -DBUILD_SHARED_LIBS=off -DGMX_BUILD_MDRUN_ONLY=ON\ -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-C -DCMAKE_CXX_COMPILER=mpixlc -DCMAKE_C_COMPILER=mpixlcxx I have managed to build for a similar BGQ machine without problems, but I've no idea if this problem lies within GROMACS or with this machine. Many thanks, Adam --- Adam Hardy PhD Student Heriot Watt University Edinburgh Campus, Riccarton EH14 4AS +441314513074 ah...@hw.ac.uk --- -- 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] ADD_LIBRARY cmake error on Bluegene/Q
Sorry for the confusion, yes, find and replace Marenostrum with Juqeen for most of that last mail. Just got some PRACE test accounts and I got myself confused. The 2.6 version of cmake was from Marenostum before I’d loaded the proper module. Try again: Fermi (failed build, xl compiler) - cmake 2.8.8 Juqeen (successful, gnu compiler?) - cmake 2.8.10.2 I had, clearly not really knowing what I was doing, specified gnu for Juqueen but this seems to be getting overridden somehow, I’ll look into that but whatever happened my build worked. There’s no other version of cmake I can find but I’ll contact the helpdesk and see if they can make one available. If you have any other suggestions I’d love to hear them, otherwise thanks for your input. Adam On 12/02/2016, 13:50, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham" wrote: >Hi, > >On Fri, Feb 12, 2016 at 1:42 PM Hardy, Adam wrote: > >> Hi Mark, >> >> I was able to compile GROMACS on Marenostrum, the cmake version is >> "2.6-patch 2". >> > >That seems wildly unlikely. GROMACS has required CMake 2.8+ for quite a few >versions now. > >On Fermi it failed, the cmake version is "2.8.8". >> > >OK. I suggest you try a more recent version of CMake. I can build fine on >Vesta and Juqueen with e.g. 2.8.12.2, but haven't tried 2.8.8. Object >modules were a new feature in 2.8.8 (part of why we require that version) >and perhaps had some issues that have been resolved later. > >This is not necassarily a fair comparison. I compiled using gnu on >> Marenostrum as I couldn't find the xl compiler oddly and wasn't feeling >> compelled to go looking for it. > > >Marenostrum isn't even BG/Q! > > >> I'm using xl on Fermi as using gnu is another problem all together: >> >> CMake Error at cmake/gmxManageSimd.cmake:390 (message): >> Cannot compile the requested IBM QPX intrinsics. If you are compiling >> for >> BlueGene/Q with the XL compilers, use 'cmake .. >> -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-C' to set up the tool >> chain. >> >> Despite the correct file being specified and I can see the path set >> correctly in the CMakeCache.txt. >> > >gcc's never been a supported compiler for GROMACS on BG/Q. Your reports >suggest that you were compiling GROMACS 4.5 on Marenostrum. > >Mark > > >> Adam >> >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < >> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark >> Abraham >> Sent: 12 February 2016 12:06 >> To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] ADD_LIBRARY cmake error on Bluegene/Q >> >> Hi, >> >> Do the cmake versions differ? >> >> Mark >> >> On Fri, 12 Feb 2016 12:44 Hardy, Adam wrote: >> >> > Dear all, >> > >> > >> > I'm having some difficulty compiling GROMACS 5.1.1 on a Bluegene/Q >> > machine. This is using the xl compiler. >> > >> > >> > I recieve the error: >> > >> > >> > ADD_LIBRARY for library mdrun_objlib is used with the MODULE option, but >> > the target platform supports only STATIC libraries. Building it STATIC >> > instead. This may lead to problems. >> > -- Configuring done >> > CMake Error at src/programs/CMakeLists.txt:45 (add_executable): >> > Objects of target "mdrun_objlib" referenced but is not an OBJECT >> library. >> > >> > If I attempt to compile it, it fails: >> > >> > Linking CXX executable ../../bin/mdrun_mpi_d >> > CMakeFiles/mdrun.dir/mdrun_main.cpp.o:(.toc+0x0): undefined reference to >> > `gmx_mdrun(int, char**)' >> > >> > My cmake command is as follow: >> > >> > export >> CMAKE_PREFIX_PATH=/cineca/prod/libraries/fftw/3.3.3/bgq-xl--1.0/lib/ >> > export FLAGS="-O3 -qarch=qp -qtune=qp" >> > export >> FFTW_INC_DIR=/cineca/prod/libraries/fftw/3.3.3/bgq-xl--1.0/include/ >> > export INSTALL_PRE=/fermi/home/userexternal/hbock000/gmx/ >> > >> > cmake ../ -DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_GPU=OFF -DGMX_X11=OFF >> > -DGMX_DOUBLE=ON \ >> > -DCMAKE_C_FLAGS="$FLAGS" -DCMAKE_CXX_FLAGS="$FLAGS" >> > -DGMX_BUILD_MDRUN_ONLY=ON \ >> > -DFFTW_INCLUDE_DIR=$FFTW_INC_DIR \ >> > -DCMAKE_INSTALL_PREFIX=$INSTALL_PRE -DBUILD_SHARED_LIBS=off >> > -DGMX_BUILD_MDRUN_ONLY=ON\ >&
Re: [gmx-users] correct rlist and Verlet scheme
There are people more qualified than me to explain the fine details of this, but in brief: Verlet on it's own doesn't adjust rvdw or rcoloumb (rcoulomb may be adjusted if you rae using PME for the coulomb interactions), but by default it will adjust the neighbour list cut-off (rlist) to remain with a specified energy tolerance given by verlet-buffer-tolerance. You can overide this behaviour and manually set rlist by setting verlet-buffer-tolerance=-1. Whether you want to or not will depend on why the forcefield has specified that cut-off, it may well be to achieve the same purpose, which is to propely catch interactions between atoms which move in or out of the cut-off radii between rlist update steps. Adam From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Timofey Tyugashev Sent: 12 February 2016 12:47 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] correct rlist and Verlet scheme I have trouble in correctly setting cut-offs with Verlet scheme to match force-field specific settings. It automatically adjusts cut-off and it looks like they change their values from ones recommended for the force field. Is there a way to correct it and set up them properly? The paper on FF lists 1.0 nm for short-range electrostatic and LJ interactions. The cut-off of pairlists is 1.05 nm. The forcefield is 99SB-ILDN and is present in GROMACS 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. -- 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] ADD_LIBRARY cmake error on Bluegene/Q
Hi Mark, I was able to compile GROMACS on Marenostrum, the cmake version is "2.6-patch 2". On Fermi it failed, the cmake version is "2.8.8". This is not necassarily a fair comparison. I compiled using gnu on Marenostrum as I couldn't find the xl compiler oddly and wasn't feeling compelled to go looking for it. I'm using xl on Fermi as using gnu is another problem all together: CMake Error at cmake/gmxManageSimd.cmake:390 (message): Cannot compile the requested IBM QPX intrinsics. If you are compiling for BlueGene/Q with the XL compilers, use 'cmake .. -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-C' to set up the tool chain. Despite the correct file being specified and I can see the path set correctly in the CMakeCache.txt. Adam From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham Sent: 12 February 2016 12:06 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] ADD_LIBRARY cmake error on Bluegene/Q Hi, Do the cmake versions differ? Mark On Fri, 12 Feb 2016 12:44 Hardy, Adam wrote: > Dear all, > > > I'm having some difficulty compiling GROMACS 5.1.1 on a Bluegene/Q > machine. This is using the xl compiler. > > > I recieve the error: > > > ADD_LIBRARY for library mdrun_objlib is used with the MODULE option, but > the target platform supports only STATIC libraries. Building it STATIC > instead. This may lead to problems. > -- Configuring done > CMake Error at src/programs/CMakeLists.txt:45 (add_executable): > Objects of target "mdrun_objlib" referenced but is not an OBJECT library. > > If I attempt to compile it, it fails: > > Linking CXX executable ../../bin/mdrun_mpi_d > CMakeFiles/mdrun.dir/mdrun_main.cpp.o:(.toc+0x0): undefined reference to > `gmx_mdrun(int, char**)' > > My cmake command is as follow: > > export CMAKE_PREFIX_PATH=/cineca/prod/libraries/fftw/3.3.3/bgq-xl--1.0/lib/ > export FLAGS="-O3 -qarch=qp -qtune=qp" > export FFTW_INC_DIR=/cineca/prod/libraries/fftw/3.3.3/bgq-xl--1.0/include/ > export INSTALL_PRE=/fermi/home/userexternal/hbock000/gmx/ > > cmake ../ -DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_GPU=OFF -DGMX_X11=OFF > -DGMX_DOUBLE=ON \ > -DCMAKE_C_FLAGS="$FLAGS" -DCMAKE_CXX_FLAGS="$FLAGS" > -DGMX_BUILD_MDRUN_ONLY=ON \ > -DFFTW_INCLUDE_DIR=$FFTW_INC_DIR \ > -DCMAKE_INSTALL_PREFIX=$INSTALL_PRE -DBUILD_SHARED_LIBS=off > -DGMX_BUILD_MDRUN_ONLY=ON\ > -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-C > -DCMAKE_CXX_COMPILER=mpixlc -DCMAKE_C_COMPILER=mpixlcxx > > > I have managed to build for a similar BGQ machine without problems, but > I've no idea if this problem lies within GROMACS or with this machine. > > > Many thanks, > > > Adam > > --- > > Adam Hardy > > PhD Student > > Heriot Watt University > > Edinburgh Campus, Riccarton > > EH14 4AS > > +441314513074 > > ah...@hw.ac.uk > > --- > -- > 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] ADD_LIBRARY cmake error on Bluegene/Q
Dear all, I'm having some difficulty compiling GROMACS 5.1.1 on a Bluegene/Q machine. This is using the xl compiler. I recieve the error: ADD_LIBRARY for library mdrun_objlib is used with the MODULE option, but the target platform supports only STATIC libraries. Building it STATIC instead. This may lead to problems. -- Configuring done CMake Error at src/programs/CMakeLists.txt:45 (add_executable): Objects of target "mdrun_objlib" referenced but is not an OBJECT library. If I attempt to compile it, it fails: Linking CXX executable ../../bin/mdrun_mpi_d CMakeFiles/mdrun.dir/mdrun_main.cpp.o:(.toc+0x0): undefined reference to `gmx_mdrun(int, char**)' My cmake command is as follow: export CMAKE_PREFIX_PATH=/cineca/prod/libraries/fftw/3.3.3/bgq-xl--1.0/lib/ export FLAGS="-O3 -qarch=qp -qtune=qp" export FFTW_INC_DIR=/cineca/prod/libraries/fftw/3.3.3/bgq-xl--1.0/include/ export INSTALL_PRE=/fermi/home/userexternal/hbock000/gmx/ cmake ../ -DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_GPU=OFF -DGMX_X11=OFF -DGMX_DOUBLE=ON \ -DCMAKE_C_FLAGS="$FLAGS" -DCMAKE_CXX_FLAGS="$FLAGS" -DGMX_BUILD_MDRUN_ONLY=ON \ -DFFTW_INCLUDE_DIR=$FFTW_INC_DIR \ -DCMAKE_INSTALL_PREFIX=$INSTALL_PRE -DBUILD_SHARED_LIBS=off -DGMX_BUILD_MDRUN_ONLY=ON\ -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-C -DCMAKE_CXX_COMPILER=mpixlc -DCMAKE_C_COMPILER=mpixlcxx I have managed to build for a similar BGQ machine without problems, but I've no idea if this problem lies within GROMACS or with this machine. Many thanks, Adam --- Adam Hardy PhD Student Heriot Watt University Edinburgh Campus, Riccarton EH14 4AS +441314513074 ah...@hw.ac.uk --- -- 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] H-REMD in umbrella sampling
Hi, Thank you for the advice. Though, I am a bit confused how one could implement such particles in practice. What do you understand by “make two virtual particles” ? Where it should be defined in gromacs inputs ? Also, as I understand, if I run standard umbrella sampling simulation with the pulling code in gromacs, it is already using such approach (COM pulling). I suppose that the issue here is how to force gromacs to treat different distances between COMs (and therefore different pulling potential leading to different Hamiltonian) as an argument for REMD (H-REMD in this case) and perform exchange between the umbrella windows. Since there is no answer from gromacs developers I assume that the above is not yet implemented and based on the http://redmine.gromacs.org/issues/1335 <http://redmine.gromacs.org/issues/1335> the implementation is postponed for the “future”. Thus, anyone trying to use such feature should look for solution elsewhere. Thank you. Best regards, Adam > On 23 Nov 2015, at 17:12, Yuri Garmay wrote: > > One can make two virtual particles at COMs of corresponding molecules > and set harmonic potential between them with different length for > lambdas 0 and 1. > > -- > Best regards, > Yuri > -- > 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] H-REMD in umbrella sampling
Hi, I posted a question about Hamiltonian REMD in umbrella sampling simulations on 20.11.2015 but haven't got any answer yet. In the meantime I found a topic on gromacs redmine which is related to my post: http://redmine.gromacs.org/issues/1335. May I ask what is the current status of the support of Hamiltonian replica exchange with umbrella sampling ? Thank you. Best regards, Adam -- 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] H-REMD in umbrella sampling
Hi, Is Hamiltonian REMD possible with umbrella sampling in pure gromacs 5.1 without plumed patch ? It should be according to gromacs 5 paper and manual but no details are provided of how to use it. If yes, does anyone successfully applied it and could share sample mdp options used to exchange between umbrella windows ? So far, whatever setup I use I get the message that systems are identical and there is nothing to exchange - seems that gromacs doesn’t recognise any differences in pulling options. Thanks a lot for help! Regards, Adam -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Running ultiple job in core?
If you only have the one GPU, then both simulations will be trying to share the GPU resource, so they will not be able to obtain the same performance compared to running them separately. The only true solution is to use a second GPU. You may or may not find it useful to run one of your simulations with the GPU and one without, you can force a simulation to run CPU only by using: -nb CPU. Adam > On 19 Nov 2015, at 02:45, RJ wrote: > > Hi there, > > > I have 24 threads in my PC with one GTX 980Ti GPU. I would like to run two > simulation job by assigning 12 threads for each job. I have tried using > "-ntomp 12 -ntmpi 1" for mentioning the threads and gpu. However, i couldnt > get the similar speed as if run them alone with 12 threads. I have even used > "-pin on" but haven't get any significant changes in the speed? > > > Its much appreciated if you could provide the hints on it. Thanks 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. - We invite research leaders and ambitious early career researchers to join us in leading and driving research in key inter-disciplinary themes. Please see www.hw.ac.uk/researchleaders for further information and how to apply. Heriot-Watt University is a Scottish charity registered under charity number SC000278. -- 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] Pressure from Ke and Virial from .edr
Dear All, As part of my work I need to recalculate the pressure from the kinetic energy and virial. I start with the equation (2/V)(Ke – Vir). The units given for the virial and kinetic energy (as taken from the .edr file) are given in kJ/mol so when I calculate the values of the pressure components and convert units I’m left with a pressure in Bar/mol (kJ/m^3 mol -> 10^3 Pa/mol -> 10^-2 Bar/mol). My initial thought was to multiply by Avogadro’s number but this gives me a number that is~750 times too large so clearly I’m missing something. Where am I going wrong? Many thanks, Adam -- Adam Hardy PhD Student School of Engineering and Physical Sciences Heriot Watt University Edinburgh, EH14 4AS Phone: +441314513074 ah...@hw.ac.uk<mailto:ah...@hw.ac.uk> -- - We invite research leaders and ambitious early career researchers to join us in leading and driving research in key inter-disciplinary themes. Please see www.hw.ac.uk/researchleaders for further information and how to apply. Heriot-Watt University is a Scottish charity registered under charity number SC000278. -- 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] Simulation with ligand on protein surface
Hi Justin and sorry for the vagueness What I'm observing are displacements from the binding site (granted, they are quite shallow) and loss of any relation to the experimental data. They also happen fairly fast (often below 10ns) and just looking at the trajectory, makes me think something is wrong (e.g. a nicely buried phenyl ring being exposed into the solvent). Now that you mention it, the ligand parametrization does seem like the place to look. Any hints regarding that (acpype/antechamber or otherwise) ? Thanks and a nice weekend, Adam On 07/10/2015 11:09 PM, Justin Lemkul wrote: On 7/10/15 5:02 AM, az wrote: Hi all I was wondering if anyone had experience/pointers regarding simulating protein-ligand systems where the interface was heavily surface-exposed ? I've been running quite a few of those these days with Amber99SB--ildn, TIP3P, and acpype (i.e. Ambertools) for ligand parametrization, mainly for the purpose of probing stability of peptidomimetic docking poses (10-50ns; aside from the force-field I follow Justin Lemkul's tutorial quite closely). Having however noticed that some of my reference ligands (i.e. ones with crystallographic/NMR data) wander away from where they should remain, I started wondering whether there could be something wrong with my setup. I obviously understand there's a zillion possibilities here, but I was still wondering whether there exists some sort of 'good-practice' for such cases (e.g. choice of force-fields, equilibration protocols ... anything really). I cannot be the only one doing this and if anyone has a protocol that served them well in the past, I'd love to learn about it. In general, if an interaction is not preserved, that suggests a poor parametrization of that ligand. But "wander away" is a bit vague; if it's just a small reorientation or something, it may not actually be "wrong" at all. Depends on the quality of the experimental data and the agreement with experimental conditions, as well. -Justin -- 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] 5.0 Benchmark
Hello I was looking for GROMACS benchmarks and I saw the new 5.0 benchmark results at: http://www.gromacs.org/@api/deki/files/240/=gromacs-5.0-benchmarks.pdf >From a quick read there aren't many details about the benchmarks themselves. Are the scripts and data used for these runs publicly available, or is that something still being worked on, as implied in the comment in the installation instructions? I would like to be able to include an up to date GROMACS benchmark in an upcoming evaluation. Best Wishes, Adam Huffman -- 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] Importing a trajectory into MOE
Hi Does anyone have experience/tips/ideas about importing a Gromacs trajectory into MOE ? I can obviously port everything into PDBs but between the fact that MOE cannot read multi-frame PDBs and that a lot of the functionality is restricted to dcd/mdb input, that's not exactly optimal. I got as far as converting the xtc into dcd with VMD/Wordom (MOE supports NAMD input) but it still won't load due to an 'Illegal DCD header' or lack of 'simulation starting moe file'. Thanks and kind regards, Adam -- 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] Pressure coupling error
You also need to add a second value for compressibility as you have done for tau-p and ref-p. Adam Hardy PhD Student School of Engineering and Physical Sciences Heriot-Watt University Edinburgh EH14 4AS, UK From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Riccardo Concu [ric.co...@gmail.com] Sent: 13 January 2015 15:28 To: gmx-us...@gromacs.org Subject: [gmx-users] Pressure coupling error Hi all, I’m receiving this error from grompp: ERROR 1 [file npt.mdp, line 50]: Pressure coupling not enough values (I need 2) I think I’ve inserted in the .mdo the required values: integrator = md tinit= 0 dt = 0.002 nsteps = 5000;100ns comm-mode= Linear nstcomm = 10 comm-grps= System nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstenergy= 80 nstxtcout= 750 xtc-precision= 1500 xtc-grps = System energygrps = WAT MET HEX nstlist = 20 ns_type = grid pbc = xyz periodic_molecules = no rlist= 1.1 coulombtype = PME rcoulomb = 1.1 ;cutoff-scheme = Verlet vdw-type = Cut-off rvdw = 1.5 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 6 ewald_rtol = 1e-5 optimize_fft = yes Tcoupl = Nose-hoover tc-grps = WAT MET HEX tau_t= 0.1 0.1 0.1 ref_t= 298 298 298 Pcoupl = Parrinello-Rahman Pcoupltype = semiisotropic tau_p= 1.0 1.0 ref_p = 1.0 1.0 compressibility = 4.5e-5 gen_vel = no gen_temp = 298 gen_seed = 173529 constraints = all-bonds constraint-algorithm = Lincs lincs-order = 4 lincs-iter = 1 -- 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. - We invite research leaders and ambitious early career researchers to join us in leading and driving research in key inter-disciplinary themes. Please see www.hw.ac.uk/researchleaders for further information and how to apply. Heriot-Watt University is a Scottish charity registered under charity number SC000278. -- 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] Virial Calculation in Gromacs Source Code
Dear All, As part of my work I am looking at making modifications to calculation of the virial in gromacs. I have spent some time making myself a bit familiar with the gromacs source and I've looked at the doxygen generated docs and through the various pages on the developer section of the website but I'm still at a bit of a loss as to where to start making these modifications. I've found a calc_vir.c source file and tried to follow the backwards and I also see references to the virial in do_md and global_stat but I'm struggling to put it all together. Are there any more sources of information about the source code that I haven't found or can anyone point me to where I need to be looking to make changes to the virial calculation? Thanks in advance, Adam Hardy PhD Student School of Engineering and Physical Sciences Heriot-Watt University Edinburgh EH14 4AS, UK - We invite research leaders and ambitious early career researchers to join us in leading and driving research in key inter-disciplinary themes. Please see www.hw.ac.uk/researchleaders for further information and how to apply. Heriot-Watt University is a Scottish charity registered under charity number SC000278. -- 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] Option to run mdrun without GPUs
Dear Gromacs Users, I have a version of Gromacs 5 installed with GPU support. With the setup of my system I would find it useful to occasaionaly run simulations without either of the GPUs, is there an easy way to do this (such as a flag to pass to mdrun) as I can't find one? Otherwise do I just need to compile a seperate executable without GPU support? Thanks, Adam Hardy PhD Student School of Engineering and Physical Sciences Heriot-Watt University Edinburgh EH14 4AS, UK - We invite research leaders and ambitious early career researchers to join us in leading and driving research in key inter-disciplinary themes. Please see www.hw.ac.uk/researchleaders for further information and how to apply. Heriot-Watt University is a Scottish charity registered under charity number SC000278. -- 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] Lithium Ions in Gromos53A6
Dear All, I find myself requiring lithium ions in a simulation using (a variant of) the Gromos53A6 forcefield. Chaging forcefields is not an appealing proposition due to the time already invested in the current one, so I was wondering had any suggestions or has perhaps gone to the effort of creating parameters for it? Thanks, Adam Hardy PhD Student School of Engineering and Physical Sciences Heriot-Watt University Edinburgh EH14 4AS, UK - We invite research leaders and ambitious early career researchers to join us in leading and driving research in key inter-disciplinary themes. Please see www.hw.ac.uk/researchleaders for further information and how to apply. Heriot-Watt University is a Scottish charity registered under charity number SC000278. -- 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] Box Vectors in .gro file
Dear all, I'm trying to set up a simulation which uses a parallelepiped box. The trouble I'm having is I don't quite understand the notation used to describe it in the .gro file. I have read the detail here: http://manual.gromacs.org/current/online/gro.html but it's not quite enough for me. I am sure it's some sort of standard notation but I've not come across before and every time I go searching for "box vectors" or similar I just get a lot of pages about cardboard vector art. Could someone give an explanation or point me to somewhere I can learn about this? Thanks, Adam Hardy PhD Student School of Engineering and Physical Sciences Heriot-Watt University Edinburgh EH14 4AS, UK - We invite research leaders and ambitious early career researchers to join us in leading and driving research in key inter-disciplinary themes. Please see www.hw.ac.uk/researchleaders for further information and how to apply. Heriot-Watt University is a Scottish charity registered under charity number SC000278. -- 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] gen-pairs, nrexcl and [ pairs ] in itp files
Bogdan, I had found that a little while ago but was unable to find again so thankyou for pointing me to it again and writing it in the first place. Jon, I hadn't found those file previously and they are consistent with what I have come up with independently so I guess that is a good sign. Out of interest do you use GLYCAM with GROMACS? It's something I have wanted to try but couldn't see a way to implement the different LJ scaling factors into GROMACS that seem to be required for systems with both carbohydrate and non-carbohydrate molecules. Adam Hardy PhD Student School of Engineering and Physical Sciences Heriot-Watt University Edinburgh EH14 4AS, UK From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Jon Kapla [jon.ka...@mmk.su.se] Sent: 12 May 2014 12:45 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] gen-pairs, nrexcl and [ pairs ] in itp files Hi, There have been some efforts of trying to implement the 56Acarbo before, and there are some files that you might want to take a look at in the user contributions section on the Gromacs website. I think the files there only delas with 1-4 glycosidic linkages, but I guess it should be straightforward to extend it to other connections using the dihedral types from the 56Acarbo paper. Anyway the files might come in handy for you if you haven't dicovered them yet. I can't say anything about the quality of the conversion though, since I haven't used those parameters myself, but it seems they use the same approach as you do (and as I did a couple of years ago trying to accomplish the same thing, but I swiched to Glycam parameters before I finished the project). I guess the best thing would be to try to get hold of single point energies from gromos and compare them with your conversion. http://www.gromacs.org/Downloads/User_contributions/Force_fields Regards Jon Kapla On 2014-05-12 12:49, Hardy, Adam wrote: > Dear All, > > I am attempting to make modifications to the Gromos 53A6 forcefield in order > to implement the Gromos 56Acarbo forcefield in GROMACS. Most of the > modifications are straightforward except for some of the LJ parameters. As > well as simple adjustments to most of the 1-4 interaction parameters there is > a requirement to implement a) some 1-4 interaction parameters when the 2 and > 3 atoms are specific combinations and b) some 1-5 special parameters. > > As I'm fairly new to GROMACS I was hoping someone could verify my method and > clarify one or two things. > > I would need to set nrexcl to 4 in order to stop the special 1-5 parameters > being calculated twice (once "normal" LJ, one "special"). > > In the itp file I would then need to explicitly provide all the special 1-4 > and all the 1-5 LJ parameters (in addition to listing the normal 1-4 > interaction pairs) as GROMACS cannot look these up in the forcefield files. > > If gen-pairs is set to yes, does it overwrite parameters given in the itp > file? This way I would not have to go through and explicitly list the > "normal" 1-4 interaction parameters in the itp file. > > I hope that is clear. > > Many thanks in advance, > > Adam Hardy > PhD Student > School of Engineering and Physical Sciences > Heriot-Watt University > Edinburgh EH14 4AS, UK > > > - > Sunday Times Scottish University of the Year 2011-2013 > Top in the UK for student experience > Fourth university in the UK and top in Scotland (National Student Survey 2012) > > We invite research leaders and ambitious early career researchers to > join us in leading and driving research in key inter-disciplinary themes. > Please see www.hw.ac.uk/researchleaders for further information and how > to apply. > > Heriot-Watt University is a Scottish charity > registered under charity number SC000278. > -- 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. - Sunday Times Scottish University of the Year 2011-2013 Top in the UK for student experience Fourth university in the UK and top in Scotland (National Student Survey 2012) We invite research leaders and ambitious early career researchers to join us in leading and driving research in key inter-disciplinary themes. Please see www.hw.ac.uk/researchleaders for further information and how to apply. Heriot-Watt University is a Scottish charity registered under charity number SC000278. -- Gromacs Users mailing list * Please search the archi
[gmx-users] gen-pairs, nrexcl and [ pairs ] in itp files
Dear All, I am attempting to make modifications to the Gromos 53A6 forcefield in order to implement the Gromos 56Acarbo forcefield in GROMACS. Most of the modifications are straightforward except for some of the LJ parameters. As well as simple adjustments to most of the 1-4 interaction parameters there is a requirement to implement a) some 1-4 interaction parameters when the 2 and 3 atoms are specific combinations and b) some 1-5 special parameters. As I'm fairly new to GROMACS I was hoping someone could verify my method and clarify one or two things. I would need to set nrexcl to 4 in order to stop the special 1-5 parameters being calculated twice (once "normal" LJ, one "special"). In the itp file I would then need to explicitly provide all the special 1-4 and all the 1-5 LJ parameters (in addition to listing the normal 1-4 interaction pairs) as GROMACS cannot look these up in the forcefield files. If gen-pairs is set to yes, does it overwrite parameters given in the itp file? This way I would not have to go through and explicitly list the "normal" 1-4 interaction parameters in the itp file. I hope that is clear. Many thanks in advance, Adam Hardy PhD Student School of Engineering and Physical Sciences Heriot-Watt University Edinburgh EH14 4AS, UK - Sunday Times Scottish University of the Year 2011-2013 Top in the UK for student experience Fourth university in the UK and top in Scotland (National Student Survey 2012) We invite research leaders and ambitious early career researchers to join us in leading and driving research in key inter-disciplinary themes. Please see www.hw.ac.uk/researchleaders for further information and how to apply. Heriot-Watt University is a Scottish charity registered under charity number SC000278. -- 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] Atomistic Simulation
You don't need to. Gromacs accepts pdb, gro and several other coordinate file formats. On 4 Dec 2013 14:30, panzu wrote: so How do I convert from .pdb to .gro? -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013059.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. - Sunday Times Scottish University of the Year 2011-2013 Top in the UK for student experience Fourth university in the UK and top in Scotland (National Student Survey 2012) We invite research leaders and ambitious early career researchers to join us in leading and driving research in key inter-disciplinary themes. Please see www.hw.ac.uk/researchleaders for further information and how to apply. Heriot-Watt University is a Scottish charity registered under charity number SC000278. -- 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] Atomistic Simulation
I've just started doing atomistic simulations over the last few weeks as well and can share what I've learned so far. I have been using 'automated topology builder'. It only uses the gromos 53a6 forcefield so eliminates the choice if you want to use it. ATB generates the pdb and itp files for you. There are a lot of molecules already on there or you can submit you're own using a java script molecule builder. There may well be other ways to do this but I haven't found them yet. On 3 Dec 2013 10:14, panzu wrote: Hello to everybody, I am new in atomistic simulations and a have some doubts about how to do it. I wanna simulate a mixture of Cyclohexane, Toluene and Dodecane. My questions are, ¿Where do I get the pdb files of these molecules from? and ¿How do I know which force field I should choose in pdb2gmx in order to make the itp file? Thanks in advance, Panzu -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. - Sunday Times Scottish University of the Year 2011-2013 Top in the UK for student experience Fourth university in the UK and top in Scotland (National Student Survey 2012) We invite research leaders and ambitious early career researchers to join us in leading and driving research in key inter-disciplinary themes. Please see www.hw.ac.uk/researchleaders for further information and how to apply. Heriot-Watt University is a Scottish charity registered under charity number SC000278. -- 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] valid command line argument do i use by mdrun_mpi_d for 8 cores.
As far as I understand, if you have configured it correctly with that version, it will use all available cores unless you specify otherwise. The precise command for this escapes me for the moment but it is documented on the gromacs website. When you run mdrun it will tell you how many threads it is using. On 29 Nov 2013 20:17, Mahboobeh Eslami wrote: i want to install gromacs4.6.3 on 8 core. i use following command: CMAKE_PREFIX_PATH=/usr/local/openmpi/:/home/elahe/ComTools/fftw/ cmake .. -DGMX_MPI=ON -DGMX_THREAD_MPI=ON -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_DOUBLE=ON -DCMAKE_INSTALL_PREFIX=/home/elahe/ComTools/gromacs is it correct? What command do I use to use 8 cores? which valid command line argument do i use by mdrun_mpi_d for 8 cores. thanks 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. - Sunday Times Scottish University of the Year 2011-2013 Top in the UK for student experience Fourth university in the UK and top in Scotland (National Student Survey 2012) We invite research leaders and ambitious early career researchers to join us in leading and driving research in key inter-disciplinary themes. Please see www.hw.ac.uk/researchleaders for further information and how to apply. Heriot-Watt University is a Scottish charity registered under charity number SC000278. -- 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] GMX_THREAD_MPI=ON" does not exis
You seem to be missing a -D infront of the thread mpi option. On 29 Nov 2013 16:54, Mahboobeh Eslami wrote: hi my friends, please help me i use following command for install gromacs: CMAKE_PREFIX_PATH=/usr/local/openmpi/:/home/elahe/ComTools/fftw/ cmake .. -DGMX_MPI=ON GMX_THREAD_MPI=ON -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_DOUBLE=ON -DCMAKE_INSTALL_PREFIX=/home/elahe/ComTools/gromacs but i get following error: CMake Error: The source directory "/home/elahe/.local/share/Trash/files/gromacs-4.2.6.3/build/GMX_THREAD_MPI=ON" does not exist. Specify --help for usage, or press the help button on the CMake GUI. thanks -- 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. - Sunday Times Scottish University of the Year 2011-2013 Top in the UK for student experience Fourth university in the UK and top in Scotland (National Student Survey 2012) We invite research leaders and ambitious early career researchers to join us in leading and driving research in key inter-disciplinary themes. Please see www.hw.ac.uk/researchleaders for further information and how to apply. Heriot-Watt University is a Scottish charity registered under charity number SC000278. -- 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.
