Re: [gmx-users] Problem compiling Gromacs 4.6.3 with CUDA
Ok, you convinced me. I'll really give it a try. I'm following this throw the suposition that openMP implementation on intel compilers is not as good as GNU compilers. I already tested intel openMP in our cluster, and it just sucked in comparison to the pure MPI compilation. Let's hope I can make it work together with the IMPI. I don't want to install openmpi as just a user also (did it a long time ago as root, not in limited space). Thanks again! On Fri, Nov 8, 2013 at 9:21 AM, Mark Abraham mark.j.abra...@gmail.comwrote: On Fri, Nov 8, 2013 at 12:02 AM, Jones de Andrade johanne...@gmail.com wrote: Really? Of course. With openmp gets to use all your cores for PME+bondeds+stuff while the GPU does PP. Any version without openmp gets to use one core per domain, which is bad. An what about gcc+mpi? should I expect any improvement? Run how and compared with what? Using an external MPI library within a single node is a complete waste of time compared with the alternatives (thread-MPI, OpenMP, or both). Mark On Thu, Nov 7, 2013 at 6:51 PM, Mark Abraham mark.j.abra...@gmail.com wrote: You will do much better with gcc+openmp than icc-openmp! Mark On Thu, Nov 7, 2013 at 9:17 PM, Jones de Andrade johanne...@gmail.com wrote: Did it a few days ago. Not so much of a problem here. But I compiled everything, including fftw, with it. The only error I got was that I should turn off the separable compilation, and that the user must be in the group video. My settings are (yes, I know it should go better with openmp, but openmp goes horrobly in our cluster, I don't know why): setenv CC /opt/intel/bin/icc setenv CXX /opt/intel/bin/icpc setenv F77 /opt/intel/bin/ifort setenv CMAKE_PREFIX_PATH /storage/home/johannes/lib/fftw/vanilla/ mkdir build cd build cmake .. -DGMX_GPU=ON -DCUDA_SEPARABLE_COMPILATION=OFF -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_OPENMP=OFF -DGMX_MPI=ON -DGMX_THREAD_MPI=OFF -DMPIEXEC_MAX_NUMPROCS=1024 -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_INSTALL_PREFIX=/storage/home/johannes/bin/gromacs/vanilla/ make make install cd .. rm -rf build On Thu, Nov 7, 2013 at 3:02 PM, Mark Abraham mark.j.abra...@gmail.com wrote: icc and CUDA is pretty painful. I'd suggest getting latest gcc. Mark On Thu, Nov 7, 2013 at 2:42 PM, ahmed.sa...@stfc.ac.uk wrote: Hi, I'm having trouble compiling v 4.6.3 with GPU support using CUDA 5.5.22. The configuration runs okay and I have made sure that I have set paths correctly. I'm getting errors: $ make [ 0%] Building NVCC (Device) object src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o icc: command line warning #10006: ignoring unknown option '-dumpspecs' /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In function `_start': (.text+0x20): undefined reference to `main' CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206 (message): Error generating /apps/src/gromacs/gromacs-4.6.3/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o make[2]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o] Error 1 make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2 make: *** [all] Error 2 Any help would be appreciated. Regards, Ahmed. -- Scanned by iCritical. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use
Re: [gmx-users] Problem compiling Gromacs 4.6.3 with CUDA
Did it a few days ago. Not so much of a problem here. But I compiled everything, including fftw, with it. The only error I got was that I should turn off the separable compilation, and that the user must be in the group video. My settings are (yes, I know it should go better with openmp, but openmp goes horrobly in our cluster, I don't know why): setenv CC /opt/intel/bin/icc setenv CXX /opt/intel/bin/icpc setenv F77 /opt/intel/bin/ifort setenv CMAKE_PREFIX_PATH /storage/home/johannes/lib/fftw/vanilla/ mkdir build cd build cmake .. -DGMX_GPU=ON -DCUDA_SEPARABLE_COMPILATION=OFF -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_OPENMP=OFF -DGMX_MPI=ON -DGMX_THREAD_MPI=OFF -DMPIEXEC_MAX_NUMPROCS=1024 -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_INSTALL_PREFIX=/storage/home/johannes/bin/gromacs/vanilla/ make make install cd .. rm -rf build On Thu, Nov 7, 2013 at 3:02 PM, Mark Abraham mark.j.abra...@gmail.comwrote: icc and CUDA is pretty painful. I'd suggest getting latest gcc. Mark On Thu, Nov 7, 2013 at 2:42 PM, ahmed.sa...@stfc.ac.uk wrote: Hi, I'm having trouble compiling v 4.6.3 with GPU support using CUDA 5.5.22. The configuration runs okay and I have made sure that I have set paths correctly. I'm getting errors: $ make [ 0%] Building NVCC (Device) object src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o icc: command line warning #10006: ignoring unknown option '-dumpspecs' /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In function `_start': (.text+0x20): undefined reference to `main' CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206 (message): Error generating /apps/src/gromacs/gromacs-4.6.3/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o make[2]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o] Error 1 make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2 make: *** [all] Error 2 Any help would be appreciated. Regards, Ahmed. -- Scanned by iCritical. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problem compiling Gromacs 4.6.3 with CUDA
Really? An what about gcc+mpi? should I expect any improvement? On Thu, Nov 7, 2013 at 6:51 PM, Mark Abraham mark.j.abra...@gmail.comwrote: You will do much better with gcc+openmp than icc-openmp! Mark On Thu, Nov 7, 2013 at 9:17 PM, Jones de Andrade johanne...@gmail.com wrote: Did it a few days ago. Not so much of a problem here. But I compiled everything, including fftw, with it. The only error I got was that I should turn off the separable compilation, and that the user must be in the group video. My settings are (yes, I know it should go better with openmp, but openmp goes horrobly in our cluster, I don't know why): setenv CC /opt/intel/bin/icc setenv CXX /opt/intel/bin/icpc setenv F77 /opt/intel/bin/ifort setenv CMAKE_PREFIX_PATH /storage/home/johannes/lib/fftw/vanilla/ mkdir build cd build cmake .. -DGMX_GPU=ON -DCUDA_SEPARABLE_COMPILATION=OFF -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_OPENMP=OFF -DGMX_MPI=ON -DGMX_THREAD_MPI=OFF -DMPIEXEC_MAX_NUMPROCS=1024 -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_INSTALL_PREFIX=/storage/home/johannes/bin/gromacs/vanilla/ make make install cd .. rm -rf build On Thu, Nov 7, 2013 at 3:02 PM, Mark Abraham mark.j.abra...@gmail.com wrote: icc and CUDA is pretty painful. I'd suggest getting latest gcc. Mark On Thu, Nov 7, 2013 at 2:42 PM, ahmed.sa...@stfc.ac.uk wrote: Hi, I'm having trouble compiling v 4.6.3 with GPU support using CUDA 5.5.22. The configuration runs okay and I have made sure that I have set paths correctly. I'm getting errors: $ make [ 0%] Building NVCC (Device) object src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o icc: command line warning #10006: ignoring unknown option '-dumpspecs' /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In function `_start': (.text+0x20): undefined reference to `main' CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206 (message): Error generating /apps/src/gromacs/gromacs-4.6.3/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o make[2]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o] Error 1 make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2 make: *** [all] Error 2 Any help would be appreciated. Regards, Ahmed. -- Scanned by iCritical. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GROMACS with GPU
Hi! If I may ask, but what is the gromacs version that is planned on the roadmap to begin to work with the newer version of openmm? Specially interested due to ATI support Regards Jones On Thu, Aug 18, 2011 at 10:01 PM, Szilárd Páll szilard.p...@cbr.su.sewrote: Hi, Gromacs 4.5.x works only with OpenMM 2.x. You might be able to use CUDA 4.0, but you will probably have to recompile OpenMM from source. Cheers, -- Szilárd On Fri, Aug 19, 2011 at 2:23 AM, Park, Jae Hyun nmn pa...@ornl.gov wrote: Dear GMX users, I am installing GMX 4.5.3 with GPU. But, the CUDA in my GPU machine is ver 4.0. Can I use this version of CUDA and openmm-3.1.1? Or, do I have to re-install CUDA 3.2 and openmm-2.0 as described in manual? Thank you in advance for your kind instruction. Jae H. Park === Jae Hyun Park, Ph. D. Physics Division Oak Ridge National Laboratory PO. Box 2008, MS-6372 Oak Ridge, TN 37831 Phone (865) 241-1482 E-mail pa...@ornl.gov -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gmxtest
Hi all. Sorry for waking up this subject again. But it rise a question for me: Is gmx 4 or gmx 3.3 that has a bug so? And, what is the bug concerned exactly? Buckingham interaction, 1-4 interactions, or buckingham 1-4 interactions? Thanks a lot in advance, Sincerally yours, Jones On Wed, May 27, 2009 at 1:03 AM, Mark Abraham mark.abra...@anu.edu.auwrote: Mark Abraham wrote: Simba Xiao wrote: Dear all, Does your GMX 4 past the gmxtest package in the gmx wiki ? My Gromacs 4.0.4 can not pass all the test. The test tip4p, ti4pflex and some kernel issues failed. That's normal at the moment, unfortunately. Future releases of gmxtest will probably fix the non-kernel issues, and GROMACS 4.0.5 will fix the kernel issues. Sorry, I mis-remembered something. The kernel issues were caused by a hard-to-provoke bug in 3.3.x which provided the reference trajectories. GROMACS 4.0.x are fine, but the test fails because of the flawed reference values. See bugzilla 313 for details. Mark I use standard packages and everything looks find. The simulation result are good and identical to gromacs 3.3.3. But, still it annoys me with the test result. Can somebody tell how much the test matters and can somebody tell something more than the wiki tells (It dose not explain much). Well, it does explain things, but not such that a new GROMACS user can get a useful result from existing versions of gmxtest. I'll upgrade the wiki documentation if/when a gmxtest re-release happens. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] TestBed in MPI not working
Hi everyone. Well, lets go straight to the point: last time I've installed gromacs, it was still 3.3.x and there was no testbed available yet. I've done some tests of my own and everything gone fine. I'm doing some new installations now, both gmx3.3.3 and gmx4.0.4. They weem to work pretty well in serial, but absolutelly not with mpi. A whole plethora of different errors appear. Before bothering the list with error messages, my question is: someone has successfully used it with OpenMPI or MPIch? Before questions arise, I have different test users for each, and absolutelly independent compilations. Thanks a lot for any answer in advance. Sincerally yours, Jones ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] TestBed in MPI not working
Thanks Justin. ;)
Well, I'm using a simple script to run the tests. The script follows:
**
#!/bin/tcsh
source ../../tcshrc
source /opt/chemistry/gmx404.ompi/bin/GMXRC.csh
set path=( $path /opt/mpi/ompi131/bin )
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/opt/mpi/ompi131/lib
set NCPUS = 2
set i = 1
while ($i = $NCPUS)
if ($i == 1) then
echo Single Precision Tests:
./gmxtest.pl simple #all
./gmxtest.pl clean /dev/null
echo Double Precision Tests:
./gmxtest.pl -double simple #all
./gmxtest.pl clean /dev/null
else
echo Single Precision Tests - Parallel in $i
./gmxtest.pl -np $i simple #all
./gmxtest.pl clean /dev/null
echo Double Precision Tests - Parallel in $i
./gmxtest.pl -np $i -double simple #all
#./gmxtest.pl clean /dev/null
endif
@ i++
end
**
Using just the simple tests now to try to find out where is the error.
Since the error goes everywhere, it just simplify things.
It outputs everything ok with the serial part, but it all gets really messy
in the mpi section.
In version 4.0.4, it's complaining that the grompp is not understanding the
-np flag (Invalid command line argument). Then, it doesn't even create a
mdrun.out file. I tried to google this error, but basically nothing was
found. It also can't be a mixing of compilations, since everything is done
in completelly different and independent directories.
Version 3.3.3 on the other hand already failed in so many different places
that I'm really thinking IF I'll make it available in the new cluster. :P
This has to be any sort of pretty stupid mistake so. But I'm clueless this
time. :( Any ideas?
Thanks a lot in advance! :)
Jones
On Mon, May 11, 2009 at 7:53 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Jones de Andrade wrote:
Hi everyone.
Well, lets go straight to the point: last time I've installed gromacs, it
was still 3.3.x and there was no testbed available yet. I've done some tests
of my own and everything gone fine.
I'm doing some new installations now, both gmx3.3.3 and gmx4.0.4. They
weem to work pretty well in serial, but absolutelly not with mpi. A whole
plethora of different errors appear.
Before bothering the list with error messages, my question is: someone has
successfully used it with OpenMPI or MPIch? Before questions arise, I have
different test users for each, and absolutelly independent compilations.
Every installation (serial and MPI) that I have installed worked
flawlessly. Our cluster uses mpich, and our local machines (dual-core) use
OpenMPI.
Can you provide some of the error messages? Are the reported from Gromacs,
or from the MPI implementations?
-Justin
Thanks a lot for any answer in advance.
Sincerally yours,
Jones
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--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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Re: [gmx-users] TestBed in MPI not working
Hi Justin This has been discussed several times on the list. The -np flag is no longer necessary with grompp. You don't get an mdrun.out because the .tpr file is likely never created, since grompp fails. Yes, I know that and that is what I would have expected. But what I'm running is the gmxtest.pl script. Even using the 4.0.4 version, it explicit states that I must use -np N to make parallel works on its own command line. gmxtest.pl Usage: ./gmxtest.pl [ -np N ] [-verbose ] [ -double ] [ simple | complex | kernel | pdb2gmx | all ] or: ./gmxtest.pl clean | refclean | dist I would expect that the script would use it only for mdrun and not for grompp, but it seems to try to use on both. What becomes really strange it the testbed really works. So, gmxtest.pl has a bug on 4.0.4? Or how should I really tell gmxtest.pl to test in a growing number of cores? Version 3.3.3 on the other hand already failed in so many different places that I'm really thinking IF I'll make it available in the new cluster. :P What messages are you getting from 3.3.3? I thought you said the 3.3.x series worked fine. I'll login for those and try to get any reproducible error here. ;) As soon as I have these, I post back in this thread. Thanks a lot again, Jones ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] TestBed in MPI not working
Hi Justin. Thanks a lot for that. It helped, but enough yet. :( Just made 4.0.4 tests reach the same range of errors that I'm getting with 3.3.3. :P Using openMPI, it just complains that it can't find orted. That would mean that the paths are not in there, BUT they are. :P If I just try to run orted from the command line without any arguments: * *gmxtest404 196% orted [palpatine:28366] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 125 -- It looks like orte_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during orte_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): orte_ess_base_select failed -- Returned value Not found (-13) instead of ORTE_SUCCESS -- [palpatine:28366] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file orted/orted_main.c at line 323 ** So, the shell IS finding the file. But when I do it not from the script anymore (I was already thinking in something on the it-else-end stack), all mpi tests fail with the following message on mdrun.out file: ** *orted: Command not found. -- A daemon (pid 27972) died unexpectedly with status 1 while attempting to launch so we are aborting. There may be more information reported by the environment (see above). This may be because the daemon was unable to find all the needed shared libraries on the remote node. You may set your LD_LIBRARY_PATH to have the location of the shared libraries on the remote nodes and this will automatically be forwarded to the remote nodes. -- -- mpirun noticed that the job aborted, but has no info as to the process that caused that situation. -- mpirun: clean termination accomplished *** What is going on? Next thing I think about doing is to execute a full command line from one of the tests directly, to see that it works... :( :P Now I'm absolutelly lost. Any ideas, please? Thanks a lot, Jones On Mon, May 11, 2009 at 9:07 PM, Justin A. Lemkul jalem...@vt.edu wrote: Justin A. Lemkul wrote: Jones de Andrade wrote: Hi Justin This has been discussed several times on the list. The -np flag is no longer necessary with grompp. You don't get an mdrun.out because the .tpr file is likely never created, since grompp fails. Yes, I know that and that is what I would have expected. But what I'm running is the gmxtest.pl script. Even using the 4.0.4 version, it explicit states that I must use -np N to make parallel works on its own command line. gmxtest.pl Usage: ./gmxtest.pl [ -np N ] [-verbose ] [ -double ] [ simple | complex | kernel | pdb2gmx | all ] or: ./gmxtest.pl clean | refclean | dist I would expect that the script would use it only for mdrun and not for grompp, but it seems to try to use on both. What becomes really strange it the testbed really works. So, gmxtest.pl has a bug on 4.0.4? Or how should I really tell gmxtest.pl to test in a growing number of cores? Ah, sorry for the mis-read :) There is a simple fix that you can apply to the gmxtest.pl script: % diff gmxtest.pl gmxtest_orig.pl 161c161 system($grompp -maxwarn 10 $ndx grompp.out 21); --- system($grompp -maxwarn 10 $ndx $par grompp.out 21); -Justin Version 3.3.3 on the other hand already failed in so many different places that I'm really thinking IF I'll make it available in the new cluster. :P What messages are you getting from 3.3.3? I thought you said the 3.3.x series worked fine. I'll login for those and try to get any reproducible error here. ;) As soon as I have these, I post back in this thread. Thanks a lot again, Jones -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send
Re: [gmx-users] TestBed in MPI not working
Ok, summary of errors begin here. First, errors with MPI in double precision: 1 Simple Test: bham: ns type Simple is not supported with domain decomposition, use particle decomposition: mdrun -pd 7 Complex Tests: acetonitrilRF: ns type Simple is not supported with domain decomposition, use particle decomposition: mdrun -pd aminoacids: ns type Simple is not supported with domain decomposition, use particle decomposition: mdrun -pd argon: ns type Simple is not supported with domain decomposition, use particle decomposition: mdrun -pd sw: ns type Simple is not supported with domain decomposition, use particle decomposition: mdrun -pd tip4p: ns type Simple is not supported with domain decomposition, use particle decomposition: mdrun -pd urea: ns type Simple is not supported with domain decomposition, use particle decomposition: mdrun -pd water: ns type Simple is not supported with domain decomposition, use particle decomposition: mdrun -pd 16 Kernel Tests: 0 computation time. Something gone REALLY bad on those... :( Except for the kernel tests, (seems that) in all I'm getting that same error message (still looking at it). Are those expected to appear? And the kernel ones? Am I wrong, or that means compilation problems (specially because they appear in all tests, single and double precision, with and withou MPI). Also getting error in serial in single precision in 4 complex tests. Those seems to have run, but yelded wrong results? Does anybody has any clue, please? Shall I go straight to recompilation, despite there is no reason for failure here? Thanks a lot! Jones On Mon, May 11, 2009 at 10:42 PM, Jones de Andrade johanne...@gmail.comwrote: Hi Justin. Well, bothering again. Good and bad news. The good news: I found a strange work-around for my problems here. For some reason, the perl script updates the path, environments and everything else when runs. So, the variables I placed on the script I was using where simply lost. Workaround here was, then, to just include those in the .tcshrc file and log again. The problem is that it's not pratical. I'm trying a lot of different MPIs and libraries compilations, and having to edit that file, and or logou/login or source it, is not pratical at all. Is there any other way, so that the perl script will be happy with the variables it has when its called, instead of initializing all them again? Second, here comes the real bad news: Lots of erros. Without MPI, in single precision, 4 complex and 16 kernel tests fail. Without MPI, but in double precision, just the 16 kernel tests fail. With MPI, in single precision, it fails on 1 simple, 9 complex and 16 kernel tests! And with MPI and double precision, 1 simple, 7 complex and 16 kernel tests fails. :P Edit: Just received your message. Well, it seems that I've done a mistake on my script, but since at least part of the tests worked, it means that it's not the MPI that is, at least, missconfigured. I will look deeper into the erros above, and tell you later. Thanks a lot, Jones On Mon, May 11, 2009 at 9:41 PM, Jones de Andrade johanne...@gmail.comwrote: Hi Justin. Thanks a lot for that. It helped, but enough yet. :( Just made 4.0.4 tests reach the same range of errors that I'm getting with 3.3.3. :P Using openMPI, it just complains that it can't find orted. That would mean that the paths are not in there, BUT they are. :P If I just try to run orted from the command line without any arguments: * *gmxtest404 196% orted [palpatine:28366] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 125 -- It looks like orte_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during orte_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): orte_ess_base_select failed -- Returned value Not found (-13) instead of ORTE_SUCCESS -- [palpatine:28366] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file orted/orted_main.c at line 323 ** So, the shell IS finding the file. But when I do it not from the script anymore (I was already thinking in something on the it-else-end stack), all mpi tests fail with the following message on mdrun.out file: ** *orted: Command not found. -- A daemon (pid 27972) died unexpectedly with status 1 while attempting to launch so we are aborting. There may be more information reported by the environment (see above). This may be because the daemon was unable to find all the needed shared libraries
Re: [gmx-users] TestBed in MPI not working
Hi Justin. On Mon, May 11, 2009 at 11:10 PM, Justin A. Lemkul jalem...@vt.edu wrote: All of the above can be fixed by changing the appropriate .mdp option. Yes, I agree. I'll try that. Probably that's what will solve that problem. If that's ok, I'll send to the site a revised version of the test set. :) Known issue: http://bugzilla.gromacs.org/show_bug.cgi?id=313 Ok, this one I would never expect coming. Since 1-4 nonbonded interations are pretty important (specially) on our studies here, does this error means that I should get back to 4.0.3 version (which is reported to NOT yeld those errors), or perharps even back to 3.3.3? Someone else just experienced this problem as well. Probably needs to be looked into. Look into thee contents of checkpot.out and checkvir.out to see if the results are similar to: http://www.gromacs.org/pipermail/gmx-users/2009-May/041696.html The problem there appeared to be a missing energy term (Vir-XX). Again here: how to deal with this issue? Go back one revision in gromacs for now, and report to bugzilla with all files this one? :) Thanks a lot for all help. Looking forward for your answer. Jones ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Nehalem
One point here is the fact that on specfp gromacs is NOT compiled with the assembly parts. Those come from fortran. Performance hit, in different ways from different architectures and compilers due to this. ;) On Fri, Feb 13, 2009 at 10:04 AM, sobereva sobju...@yahoo.com.cn wrote: Hi, Gromacs is a test term of SPEC CPU2006 benchmark suite, which aims at providing a standard and comparable performance evaluation for different platform. They provided a online database http://www.spec.org/cgi-bin/osgresults?conf=cpu2006 visit it and search the CPU name you interested, the performance on gromacs and some other scientific softwares will be listed. The performances record of the CPU based on Harpertown, Shanghai and Nehalem are now available on the database. --Lu Tian Dear All, could somebody already test the performance of Intel's Nehalem CPU in comparison to Harpertown or to AMD's Shanghai using Gromacs? Thanks Rainer __ Dr. Rainer Böckmann Theoretical Computational Membrane Biology Center for Bioinformatics Saar Universität des Saarlandes Gebäude C7.1, EG D-66041 Saarbrücken, Germany Phone: ++49 +681 302-64169 / 68627 FAX: ++49 +681 302-64180 E-Mail: rai...@bioinformatik.uni-saarland.de http://www.bioinf.uni-sb.de/RB/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Martini + other force field
Am I wrong, or are you considering some kind of MSCG (which is not into gromacs at least in a standard, straight forward out of the box way)? That's nice, would be really interesting to implement, would take long time and is still a relativelly open-field with lot to be still explored. I think we should talke a bit on private about that... :D On Tue, Feb 3, 2009 at 1:03 PM, Elton Carvalho elto...@if.usp.br wrote: On Mon, Feb 2, 2009 at 7:50 PM, XAvier Periole x.peri...@rug.nl wrote: -No: is where you can find much more arguments. First of all the two force fields have not been parametrized consistently. Second you'll probalby have problems in defining the interactions between the two approches. How the protein will interact with the membrane (and water). In Martini the interactions are effective ... What if he used some ONIOM-like approach, calculating, say, Martini energies for ther whole system, subtracting Martini energies for the small molecule and then adding opls energies for it? -- Prevaleço-me do ensejo para reiterar a Vossa Excelência protesto de elevada estima e consideração. Elton Carvalho Tel.: +55 11 3091-6881/6979 Dept Física dos Materiais e Mecânica Instituto de Física Universidade de São Paulo P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ionic liquid
Hi naimah. Sorry for the late replay, but I was travelling. What kind of ionic liquids are you interested in? If they are the dialkyl-immidazolium ones, I'm doing simulations on these systems for quite some time now (please look at these references: Journal of Physical Chemistry B, v. 112, p. 8966-8974, 2008; Journal Of Physical Chemistry B, Washington, v. 106, n. 14, p. 3546-3548, 2002; Journal Of Physical Chemistry B, Washington, v. 106, n. 51, p. 13344-13351, 2002), and already have a few of them on gromacs topology files ready (Unfortunatelly, not many due to recent problems in the computer...). What sort of data are you interested in? Regards, Jones On Sun, Nov 2, 2008 at 11:17 PM, naimah haron naimah [EMAIL PROTECTED]wrote: how to do molecular dynamics for ionic liquids by using GROMACS. Can u tell me the correct method to do molecular dynamics and which topologies are suitable for use with NMR-type calculations or all-atom force fields. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] nature of gromacs / gcc-4.x problem
Just addin my drop here: Just did the same, both single and double precision, not parallel anyway. What I get is the following: *aurora down/gmxtest 41%* ./gmxtest.pl all All 16 simple tests PASSED FAILED. Check files in dec+water 1 out of 14 complex tests FAILED All 63 kernel tests PASSED All 45 pdb2gmx tests PASSED User:54.947s Sys:13.548s Elap:1:18.66 CPU util:87.0% Memory:0k *aurora down/gmxtest 42%* ./gmxtest.pl -double all All 16 simple tests PASSED All 14 complex tests PASSED All 63 kernel tests PASSED All 45 pdb2gmx tests PASSED User:62.427s Sys:15.112s Elap:1:25.65 CPU util:90.5% Memory:0k *aurora down/gmxtest 43%* gcc -v Using built-in specs. Target: x86_64-suse-linux* . . .* gcc version* 4.3.1 20080507* (prerelease) [gcc-4_3-branch revision 135036] (SUSE Linux) *. . .* *aurora down/gmxtest 55%* more ./complex/dec+water/checkpot.out :-) G R O M A C S (-: *. . .* There are 5 terms to compare in the energy files LJ (SR) step 34: -0.21167, step 34:-0.230957 Files read succesfully Again, it looks like the same error that appears in the wiki... except that the wiki mentions two error lines in there instead of one. Also, the wiki mentions the line differently: LJ (SR) step 34: -0.176025, step 34: -0.21167 Which, on its turn, seems quite odd. I thought the first number was the standard one, has it changed between 3.3.2 and 3.3.3 gmxtest' beds? And can it be that the original problems with gcc4 has vanished with the newer versions of it? Thanks a lot, and hope it also helps. Jones On Thu, Aug 7, 2008 at 6:31 AM, David van der Spoel [EMAIL PROTECTED]wrote: [EMAIL PROTECTED] wrote: Hello, I am trying to track down the exact nature of the gcc-4.1.x / gromacs bug. I have a system on which we were forced to reinstall gromacs (3.3.1 and 3.3.3) about 2 weeks ago and I didn't realize that the default gcc was bumped to 4.1.2. I am interested because ideally we won't need to throw out the last two weeks of simulation. The installation went fine and I have just run the tests in serial single precision, which all passed (except dec+water, although that was as indicated to be actually ok on the wiki... LJ (SR) step 34: -0.21167, step 34:-0.147217) That sounds good, but I'm not sure if it is enough. I searched the archives, but a simple search for gcc is overwhelming and I couldn't find anything specific. I did find some references to the bugzilla (without links), but even when I search for gcc on bugzilla I get Zarro Boogs found. Did you select Closed bugs as well? It would indeed be great if we could do more exhaustive tests at compile time... Thanks, Chris. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] old patch for slow networks
Hi all. I'm writing this message to ask a simple and direct question: the available patch of gmx3 for slow networks, that includes the ordered-all-to-all procedures, seems fo be indicated for version 3.1. It's still necessary for slow networks using gmx3.3? Thanks a lot in advance... Sincerally yours, Jones ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Dummies usage doubts
Thanks Prof. David. I've done all that now, but at the moment I'm locked getting lots of the lovelly error: Warning: 1-4 interaction between 7 and 16 at distance 4.302 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file step 0Segmentation fault I've visually checked the .gro file, and the atoms mentioned are not from start at such crazy distances. I've included extra exclusions between the virtual sites and the atoms that are at one and two bonds away. Does it means I should include also the 1-4 in the exclusions or pair sections? Sorry, never dealt with dummy sites before this. I thought using a pre-equilibrated box with a different model would at least avoid explosion problems, so or I missing something, of this assumption was completelly wrong. Thanks a lot in advance, Sincerally yours Jones On 10/11/07, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi all. Well, I'm having a bit of trouble here because the work has decided to go in the direction of something I've never used before with gromacs: dummy atoms (or now virtual sites). I assume this is not for a protein, in which case pdb2gmx does it for you. I've got at least three questions in order to use them: 1 - does the virtual sites need to be included in the .gro files in order to make a simulation run? Yes. 2 - do I need to include them in the exclusion list? It depends, but usually yes. 3 - do I need to include them in the atoms section? Yes. Thanks a lot in advance for any help anyone can provide in these subjects. ;) Check the mannual too. Chapter 5. An dtopologies for TIP4P, TIP5P etc. Sincerally yours, Jones ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Dummies usage doubts
Hi Prof. David. What details do you mean? Actual topology files are attached. Anything else? Thanks a lot in advance! Sincerally yours, Jones On 10/11/07, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Thanks Prof. David. I've done all that now, but at the moment I'm locked getting lots of the lovelly error: Warning: 1-4 interaction between 7 and 16 at distance 4.302 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file step 0Segmentation fault please give more details... I've visually checked the .gro file, and the atoms mentioned are not from start at such crazy distances. I've included extra exclusions between the virtual sites and the atoms that are at one and two bonds away. Does it means I should include also the 1-4 in the exclusions or pair sections? Sorry, never dealt with dummy sites before this. I thought using a pre-equilibrated box with a different model would at least avoid explosion problems, so or I missing something, of this assumption was completelly wrong. Thanks a lot in advance, Sincerally yours Jones On 10/11/07, *David van der Spoel* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi all. Well, I'm having a bit of trouble here because the work has decided to go in the direction of something I've never used before with gromacs: dummy atoms (or now virtual sites). I assume this is not for a protein, in which case pdb2gmx does it for you. I've got at least three questions in order to use them: 1 - does the virtual sites need to be included in the .gro files in order to make a simulation run? Yes. 2 - do I need to include them in the exclusion list? It depends, but usually yes. 3 - do I need to include them in the atoms section? Yes. Thanks a lot in advance for any help anyone can provide in these subjects. ;) Check the mannual too. Chapter 5. An dtopologies for TIP4P, TIP5P etc. Sincerally yours, Jones ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED][EMAIL PROTECTED] mailto:[EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman
Re: [gmx-users] Dummies usage doubts
Hi Prof. David. Yes, it a self created topology. This one is based on another self created topology that runs perfectly for cyclohexane. It was adapted to include the dummy atoms. I guess there is something wrong in the definition of the dummies in the topology. But I have no clue where it is. Can you provide me some clue on this? I'll run a single molecule now. Thanks a lot in advance, Sincerally yours, Jones On 10/11/07, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi Prof. David. What details do you mean? Actual topology files are attached. Anything else? Thanks a lot in advance! Sincerally yours, Jones There is something wrong in the topology, youäll have to debug it yourself... -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Dummies usage doubts
Hi all. Just informing, I tried a single molecule, and the topology with all dummies minimize (despite taking loads of steps bfgs steps). The interesting thing is that the distance between atom 6 and 17 at beggining reads 3.1 angstrons, and at the end read 2.9 angstrons. Why it's going bad with many molecules or even single molecule MD, God? Thanks a lot everybody in advance, Sincerally yours, Jones On 10/11/07, Jones de Andrade [EMAIL PROTECTED] wrote: Hi Prof. David. Yes, it a self created topology. This one is based on another self created topology that runs perfectly for cyclohexane. It was adapted to include the dummy atoms. I guess there is something wrong in the definition of the dummies in the topology. But I have no clue where it is. Can you provide me some clue on this? I'll run a single molecule now. Thanks a lot in advance, Sincerally yours, Jones On 10/11/07, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi Prof. David. What details do you mean? Actual topology files are attached. Anything else? Thanks a lot in advance! Sincerally yours, Jones There is something wrong in the topology, youäll have to debug it yourself... -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Dummies usage doubts
Hi all. Ok, I found the erors. One small in the topology, and another huge in the .gro formating. I'll deal with a few other molecules in the next days, and hopefully I'll be able to make a small contribution to the programs library with a little add_dummies program. Will test it a bit more, though. Anyway, thanks a lot everybody for all help! :) Sincerally yours, Jones On 10/11/07, Jones de Andrade [EMAIL PROTECTED] wrote: Hi all. Just informing, I tried a single molecule, and the topology with all dummies minimize (despite taking loads of steps bfgs steps). The interesting thing is that the distance between atom 6 and 17 at beggining reads 3.1 angstrons, and at the end read 2.9 angstrons. Why it's going bad with many molecules or even single molecule MD, God? Thanks a lot everybody in advance, Sincerally yours, Jones On 10/11/07, Jones de Andrade [EMAIL PROTECTED] wrote: Hi Prof. David. Yes, it a self created topology. This one is based on another self created topology that runs perfectly for cyclohexane. It was adapted to include the dummy atoms. I guess there is something wrong in the definition of the dummies in the topology. But I have no clue where it is. Can you provide me some clue on this? I'll run a single molecule now. Thanks a lot in advance, Sincerally yours, Jones On 10/11/07, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi Prof. David. What details do you mean? Actual topology files are attached. Anything else? Thanks a lot in advance! Sincerally yours, Jones There is something wrong in the topology, youäll have to debug it yourself... -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Reading XTC files from fortran90
Hi all. First of all, I would really want want to apologize if I somehow missunderstood any previous message from anyone, and made myself a bit annoying because of this fact. Second, I would like to say thanks again to eferybody for all help in these matters. On 10/1/07, Tsjerk Wassenaar [EMAIL PROTECTED] wrote: I'd say the easiest is to get into gmx_editconf and look at the option -grasp or -mead which put the atomic charge and vdw radius in the b-factor and occupancy field of a .pdb file when given a .tpr file. It's trivial to make it write charges and masses instead. Would also be a good first exercise for C/Gromacs :p Good idea! Even I don't choose to sitck with many file type conversions for the sake of the disk space, that specific program now seems to be a good start to learn explicitly how all the topology data is passed from one place to the other. And that would help me to learn how to read the topology files (since it seems to be only a matter now of reading atomic charges and masses). I'm not sure what you mean with shape and that integer. There's nothing much redundant in the .xtc file and there are no integers having to do with box shape. In fact, there is no shape... Well, by shape I meant cubic and truncated octahedral, for example. But the integer was my mistake (old dlpoly adaptions that just came to my mind, together with the first integer in the header of all xdrf files and that I could not find a proper meaning at time), thought for a moment that the first integer in the .xtc header mean the shape of the box. Just played a bit later with the manual and recorded that it's only the 9 box parameters that are important to define that within gromacs. Sorry for that mistake. So, I would have atom names, Yes From .gro or .pdb file in the standard way. number of molecules types, No number of molecules of each type, No number of atoms of each molecule type, No I think those three can become yes in a really easy way: some kind of state machine would easily do the trick and count them properly. coordinates, Yes From .xtc or .pdb file. charges Yes, if you use the right editconf option and masses on a .pdb file, correct? No. Only modifying editconf to print those in a adapted .pdb file, throw a file conversion and much disk space wasted. Or I can learn exactly from editconf how to read it from .tpr or .top (I guess it takes from these files the atomic charges when needed) and adapt into my codes. But, still, where could I then easilly get the box type and sizes, as well as simulation times? The .xtc file, the .edr file... So .xtc, since its already under control. ;) Fine :-) That's the sort of reason that you'd want to have to keep Fortran for the present problem. So we agree here. Three ways so: converting the trajectories to another format (ugly for my taste, and too much disk space needed), linking to a library (like done in reading .xtc files) or linking to an object. ;) Like I said, the masses are easy to infer from the atom names. You don't need to read them... you know anything starting with N has mass 14.011 (or whatever it is). Or you can read share/gromacs/top/atommass.dat to do the lookups. That is the kind of stuff I really don't like. For instance, all codes I written for all this time long aimed at being abolutelly general. So, if anything starting by N means nitrogen, how to deal when someone using the same program (even in the group) chooses to say that Nb is a different type of nitrogen while another says it is niobium? The program must be able to deal with such problems that arise (and believe, I've already got locked at this one once, and that's why I don't go such a way anymore), and the only way I see it doing so is directly reading the topologies, instead of knowing it in advance. ;) Sorry for not noticing the box shape in the .xtc file. I passed over that integer in the reading, dismissing it as only some kind of old feature useless now. Really sorry for that point. Which files should I look for in order to get the proper way of reading masses and atomic charges from a .tpr file? And which objects will need to be included in the linking stage? Is there any outsider program (fortran would be perfect, but I don't think it will be too common too) that works directly with the .tpr files? tpxio.c will have relevant functions. Or, follow the execution of mdrun until it reads the .tpr file and see how it handles these things. Thanks a lot! That final information will be really usefull for me to sort out how to properly link those routines in my codes. :) If you use the editconf suggestion to get charges, you don't need to read a .tpr file. But then or I get locked into the problem of generality of having too much disk usage. But that idea will be also usefull to learn how to read the masses and charges from .tpr files. Thanks a lot everybody for all the help, and sorry for taking so much
Re: [gmx-users] Reading XTC files from fortran90
Hi Tsjerk. Thanks for the prompt answer. Good idea, I can take the atom names from a .gro file, nad, probably some strange algorithm can also get the number of atoms per molecule and number of molecules from there, am I right? That would help a lot. But: I'll still be unable to get atomic masses and point charges. No to mention the box shape. :( And I'll need a way to read these parameters too, unless I begin to write all them in a really awfull and strange index file. From what I can understand on the file logistics of gromacs, these information are only stored in the whole .top .itp .atp .rtp structure of files or, in a condensed form, in the .tpr file. Is that right? Thanks a lot for all the information and help! Sincerally yours, Jones On 9/30/07, Tsjerk Wassenaar [EMAIL PROTECTED] wrote: Hi Jones, You probably only need to read the atoms and such from a .pdb or .gro file, unless you really want to have topology information (bondedness, molecule definitions, etc). Then you do have to read the topology file or a .tpr file directly. Don't recall having seen the fortran implementations for these... But maybe Bert knows better. Just one note... There's no shape in PBC. The lattice vectors are all there is, and these are stored in the .xtc file (as you already know). Cheers, Tsjerk On 9/30/07, Jones de Andrade [EMAIL PROTECTED] wrote: Hi Bert. Thanks a lot for the help. I've found the mistakes, one programming minor issue and a compiler configuration a bit of hidden in the config files. Old time mistakes just choose to arise at its worst moments. :) At the moment, I already can read the coordinates, number of atoms, box coordinates, step number, simulation time and precision. I guess this is all what is stored in the .xtc files themselves, am I right? I have so one extra question: I guess that extra information as atom names, number of molecules of type X, number of molecular types, box and pbc shape and atomic charges and masses are *not* stored in the .xtc files, am I right? Ok, the integer stuff (number of molecules of type X, number of molecular types, box and pbc) could be written in a special .ndx file, but that would, by all means, looks at least diselegant. If so, the only two possible ways of getting them is reading or the .top and .itp files correctly, or to read the .tpr file, correct? Now, is there any guideline available on how to deal with those files? Thanks a lot everybody for all the help. Sincerally yours, Jones On 9/29/07, Bert de Groot [EMAIL PROTECTED] wrote: On Sat, 29 Sep 2007, Jones de Andrade wrote: Hi Bert. Thank you for the prompt answer. Just did as instructed, but got the following: CruNumMac src/own/B/9/xtc 286% ifort xtciof.f90 test_xtc.f90 -L/home/johannes/src/own/B/9/xtc/xtc/ -lxrdf -lg2c IPO link: can not find -lxrdf well, apparently the path you specify with -L does not contain a libxdrf.a the way you called it the compiler expects it to be located here: /home/johannes/src/own/B/9/xtc/xtc/libxdrf.a also, IIRC, the xtcio stuff is already linked into the libxdrf.a, so no need to include it again. ifort: error: problem during multi-file optimization compilation (code 1) Looks better, in the sense that the number of error messages was reduced. But still doesn't accept to link to the xrdf library. Tried that with and without re-make of the library (strange fact that the SGI arch is to be used in linux) and also tried to say -llibxrdf instead of -lxrdf. Nothing worked. Have you or someone come across such an error before? Any clue of what can possibly be going wrong? Thanks a lot in advance... Sincerally yours, Jones On 9/29/07, Bert de Groot [EMAIL PROTECTED] wrote: Hi, try: download http://www.mpibpc.gwdg.de/groups/de_groot/xtc.tar.gz (and optionally issue a 'make' in the xtc directory after unpacking) in the linking stage, use something like ifort -blabla -lxdrf -L/wherever/xtc -lg2c your smalll test code looks OK apart from the fact that I don't know what happens if you readwrite from the same file. Bert Bert Bert de Groot, PhD Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 37077 Goettingen, Germany tel: +49-551-2012308, fax: +49-551-2012302 http://www.mpibpc.gwdg.de/groups/de_groot ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests
Re: [gmx-users] Reading XTC files from fortran90
Hi all. Firstly, thanks a lot for all the help! ;) First, about reading the atom-names from a .gro file, I don't think it would so painfull. It would look like a bit to having a well programmed state machine in the code. About the language, yes, I admit that bor reads and writes, fortran is miserable. But for calculations (like the inner codes of a certain program? ;) only joking... :D ) if one chooses not to go by assembly, fortran is still the way, specially if you consider the extra simplicity of fortran90. Anyway, I would not even consider re-writing the reads in fortran, but would love to consider to link to a library (like in reading .xtc files) or gromacs compiled object just to read it correctly. ;) About the box, is it on the .xtc file? Could not get the proper variable of it, could someone give me some infor which is that? Finally: yes, I considered changing everything to a .pdb file, despite the file size and the fact that I completelly forgot it could have the charges on it. But even so I would still have problems with the atomic masses, am I right? Or can I put that on a standard pdb file with gromacs programs? Again, tahnks a lot for all help in advance! Sincerally yours, Jones On 9/30/07, David van der Spoel [EMAIL PROTECTED] wrote: Mark Abraham wrote: Jones de Andrade wrote: Hi Tsjerk. Thanks for the prompt answer. Good idea, I can take the atom names from a .gro file, nad, probably some strange algorithm can also get the number of atoms per molecule and number of molecules from there, am I right? That would help a lot. Simplest is to write a parser for a gmxdump of a .tpr file. This is what Perl was made for. If you're constrained to use Fortran for your analysis program, then developing an intermediate file format for it to parse might be worthwhile. But: I'll still be unable to get atomic masses and point charges. No to mention the box shape. :( And I'll need a way to read these parameters too, unless I begin to write all them in a really awfull and strange index file. From what I can understand on the file logistics of gromacs, these information are only stored in the whole .top .itp .atp .rtp structure of files or, in a condensed form, in the .tpr file. Is that right? Yeah. Writing something to do the lookups in the .*tp files which grompp does to form the .tpr is asking for trouble. Do the lookup in the .tpr file. The .edr file has box dimensions, of course. All this makes it sound like you should be dropping Fortran and writing in C or Perl! the box is in the xtc file, if you need the atom names a corresponding pdb or gro file should do the trick. don't try to read tpr files or gmxdumps of it, that's a complete waste of time. you can e.g. use editconf to dump a pdb file with charges in the b-factor fields. And indeed, using fortran will make your life quite miserable for these kind of things. -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Reading XTC files from fortran90
Hi Mark. Wait a second, you mean that editconf would allow me to have both charges and masses on a .pdb file directly from command line (having other matters asking for my presence absolutelly now, so please forgive me if this message becomes somehow strange) So, I would have atom names, number of molecules types, number of molecules of each type, number of atoms of each molecule type, coordinates, charges and masses on a .pdb file, correct? But, still, where could I then easilly get the box type and sizes, as well as simulation times? Thanks a lot for all the help, and sorry for this punctual hurry here. Sincerally yours, Jones On 9/30/07, Mark Abraham [EMAIL PROTECTED] wrote: David van der Spoel wrote: the box is in the xtc file, if you need the atom names a corresponding pdb or gro file should do the trick. don't try to read tpr files or gmxdumps of it, that's a complete waste of time. you can e.g. use editconf to dump a pdb file with charges in the b-factor fields. Yes, I now see that editconf has that ability, and Jones can fill in the masses himself, so he doesn't need to parse the .tpr at all. And indeed, using fortran will make your life quite miserable for these kind of things. :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Reading XTC files from fortran90
Hi Bert. Thank you for the prompt answer. Just did as instructed, but got the following: CruNumMac src/own/B/9/xtc 286% ifort xtciof.f90 test_xtc.f90 -L/home/johannes/src/own/B/9/xtc/xtc/ -lxrdf -lg2c IPO link: can not find -lxrdf ifort: error: problem during multi-file optimization compilation (code 1) Looks better, in the sense that the number of error messages was reduced. But still doesn't accept to link to the xrdf library. Tried that with and without re-make of the library (strange fact that the SGI arch is to be used in linux) and also tried to say -llibxrdf instead of -lxrdf. Nothing worked. Have you or someone come across such an error before? Any clue of what can possibly be going wrong? Thanks a lot in advance... Sincerally yours, Jones On 9/29/07, Bert de Groot [EMAIL PROTECTED] wrote: Hi, try: download http://www.mpibpc.gwdg.de/groups/de_groot/xtc.tar.gz (and optionally issue a 'make' in the xtc directory after unpacking) in the linking stage, use something like ifort -blabla -lxdrf -L/wherever/xtc -lg2c your smalll test code looks OK apart from the fact that I don't know what happens if you readwrite from the same file. Bert ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Reading XTC files from fortran90
Hi Bert. Thanks a lot for the help. I've found the mistakes, one programming minor issue and a compiler configuration a bit of hidden in the config files. Old time mistakes just choose to arise at its worst moments. :) At the moment, I already can read the coordinates, number of atoms, box coordinates, step number, simulation time and precision. I guess this is all what is stored in the .xtc files themselves, am I right? I have so one extra question: I guess that extra information as atom names, number of molecules of type X, number of molecular types, box and pbc shape and atomic charges and masses are *not* stored in the .xtc files, am I right? Ok, the integer stuff (number of molecules of type X, number of molecular types, box and pbc) could be written in a special .ndx file, but that would, by all means, looks at least diselegant. If so, the only two possible ways of getting them is reading or the .top and .itp files correctly, or to read the .tpr file, correct? Now, is there any guideline available on how to deal with those files? Thanks a lot everybody for all the help. Sincerally yours, Jones On 9/29/07, Bert de Groot [EMAIL PROTECTED] wrote: On Sat, 29 Sep 2007, Jones de Andrade wrote: Hi Bert. Thank you for the prompt answer. Just did as instructed, but got the following: CruNumMac src/own/B/9/xtc 286% ifort xtciof.f90 test_xtc.f90 -L/home/johannes/src/own/B/9/xtc/xtc/ -lxrdf -lg2c IPO link: can not find -lxrdf well, apparently the path you specify with -L does not contain a libxdrf.a the way you called it the compiler expects it to be located here: /home/johannes/src/own/B/9/xtc/xtc/libxdrf.a also, IIRC, the xtcio stuff is already linked into the libxdrf.a, so no need to include it again. ifort: error: problem during multi-file optimization compilation (code 1) Looks better, in the sense that the number of error messages was reduced. But still doesn't accept to link to the xrdf library. Tried that with and without re-make of the library (strange fact that the SGI arch is to be used in linux) and also tried to say -llibxrdf instead of -lxrdf. Nothing worked. Have you or someone come across such an error before? Any clue of what can possibly be going wrong? Thanks a lot in advance... Sincerally yours, Jones On 9/29/07, Bert de Groot [EMAIL PROTECTED] wrote: Hi, try: download http://www.mpibpc.gwdg.de/groups/de_groot/xtc.tar.gz (and optionally issue a 'make' in the xtc directory after unpacking) in the linking stage, use something like ifort -blabla -lxdrf -L/wherever/xtc -lg2c your smalll test code looks OK apart from the fact that I don't know what happens if you readwrite from the same file. Bert Bert Bert de Groot, PhD Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 37077 Goettingen, Germany tel: +49-551-2012308, fax: +49-551-2012302 http://www.mpibpc.gwdg.de/groups/de_groot ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Reading XTC files from fortran90
Hi all. I'm writing this beucase I'm having terrible problems in trying to deal with gromacs trajectory files with my own programs, originally written on fortran90. The codes themselves are enoughly big to make it out of question to try to translate them. What leads to some sort of mixed language compilation. My first guess was to try to use the guidelines from http://xray.bmc.uu.se/~spoel/md/online/xtc.html, but it absolutelly didn't worked. Could not find a compatible library. Tried to recompile gromacs in order to do so, but instead of a libsdrf.a library file, it created just common .lo and .o object files. Looked inside concoord program, as there are some mentions in the list to look at the code. Was a really good aprentize, could understand better the logics involved when dealing with .xtc files, BUT I could not use the library files that came with that. Somehow, it wasn't recognized as a valid file. My last try up to now was to try to link my test-read-program with the libxdrf object file. It yelded the following error: CruNumMac src/own/B/9/xtc 238% ifort libxdrf.lo xtciof.f90 test_xtc.f90 IPO: WARNING: no IR in object file libxdrf.lo; was the source file compiled with -ipo? IPO Error: unresolved : xdrfint_ Referenced in /tmp/ipo_ifortZNvZHh.o IPO Error: unresolved : xdrfclose_ Referenced in /tmp/ipo_ifortZNvZHh.o IPO Error: unresolved : xdrfopen_ Referenced in /tmp/ipo_ifortZNvZHh.o IPO Error: unresolved : xdrffloat_ Referenced in /tmp/ipo_ifortZNvZHh.o IPO Error: unresolved : xdrf3dfcoord_ Referenced in /tmp/ipo_ifortZNvZHh.o IPO: performing multi-file optimizations IPO: generating object file /tmp/ipo_ifortZNvZHh.o test_xtc.f90(17) : (col. 3) remark: LOOP WAS VECTORIZED. test_xtc.f90(25) : (col. 8) remark: LOOP WAS VECTORIZED. xtciof.f90(112) : (col. 3) remark: LOOP WAS VECTORIZED. libxdrf.lo: file not recognized: File format not recognized If I try to link to the .o objetc: CruNumMac src/own/B/9/xtc 240% ifort libxdrf.o xtciof.f90 test_xtc.f90 IPO: WARNING: no IR in object file libxdrf.o; was the source file compiled with -ipo? IPO Error: unresolved : xdrfint_ Referenced in /tmp/ipo_ifort2f5KMw.o IPO Error: unresolved : xdrfclose_ Referenced in /tmp/ipo_ifort2f5KMw.o IPO Error: unresolved : xdrfopen_ Referenced in /tmp/ipo_ifort2f5KMw.o IPO Error: unresolved : xdrffloat_ Referenced in /tmp/ipo_ifort2f5KMw.o IPO Error: unresolved : xdrf3dfcoord_ Referenced in /tmp/ipo_ifort2f5KMw.o IPO Error: unresolved : ffclose Referenced in libxdrf.o IPO: performing multi-file optimizations IPO: generating object file /tmp/ipo_ifort2f5KMw.o test_xtc.f90(17) : (col. 3) remark: LOOP WAS VECTORIZED. test_xtc.f90(25) : (col. 8) remark: LOOP WAS VECTORIZED. xtciof.f90(112) : (col. 3) remark: LOOP WAS VECTORIZED. /tmp/ipo_ifort2f5KMw.o(.text+0x1e1): In function `MAIN__': /tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfopen_' /tmp/ipo_ifort2f5KMw.o(.text+0x4ea):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfclose_' /tmp/ipo_ifort2f5KMw.o(.text+0x517):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfopen_' /tmp/ipo_ifort2f5KMw.o(.text+0x92b): In function `xtciof_mp_xtcheader_': /tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfint_' /tmp/ipo_ifort2f5KMw.o(.text+0x941):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfint_' /tmp/ipo_ifort2f5KMw.o(.text+0x95e):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfint_' /tmp/ipo_ifort2f5KMw.o(.text+0x97b):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrffloat_' /tmp/ipo_ifort2f5KMw.o(.text+0xb8e): In function `xtciof_mp_xtcio_': /tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrffloat_' /tmp/ipo_ifort2f5KMw.o(.text+0xbde):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrffloat_' /tmp/ipo_ifort2f5KMw.o(.text+0xc2e):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrffloat_' /tmp/ipo_ifort2f5KMw.o(.text+0xc7e):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrffloat_' /tmp/ipo_ifort2f5KMw.o(.text+0xcce):/tmp/ipo_ifort2f5KMw.f: more undefined references to `xdrffloat_' follow /tmp/ipo_ifort2f5KMw.o(.text+0xe6b): In function `xtciof_mp_xtcio_': /tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrf3dfcoord_' /tmp/ipo_ifort2f5KMw.o(.text+0xfc6): In function `xtciof_mp_xtcopen_': /tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfopen_' /tmp/ipo_ifort2f5KMw.o(.text+0x1292):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfclose_' /tmp/ipo_ifort2f5KMw.o(.text+0x12b3):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfopen_' /tmp/ipo_ifort2f5KMw.o(.text+0x134e): In function `xtciof_mp_xtccoord_': /tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrffloat_' /tmp/ipo_ifort2f5KMw.o(.text+0x139f):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrffloat_' /tmp/ipo_ifort2f5KMw.o(.text+0x13f0):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrffloat_' /tmp/ipo_ifort2f5KMw.o(.text+0x1441):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrffloat_'
[gmx-users] fortran xtc reading problem?
Hi. I'm trying to read some .xtc file trajectory files throw my fortran codes, following the guidelines from http://xray.bmc.uu.se/~spoel/md/online/xtc.html Also later found this html file on the gromacs directory here. ;) Anyway, I got stuck at some really strange point: I'm basically not finding the library xtcf to link it to. In order to be completelly right, I'm not even finding the testxtcf.f file that is supposed to be here. There was anychange in file names and/or locations between those guidelines and the actual distribution? Thanks a lot in advance! Sincerally yours, Jones ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] a future gmx 4.0 doubt
Hi Prof. Spoel. First of all, sorry for sending this message directly to your personal email address. I was concerned that opening a thread like this would lead to undesired discussions on the mail list, and I choosen to avoid it. Please, forgive me for this intrusion. I'm writing this message because I could see on the gromacs web site that the version 4.0 is coming to an end, if we can call it like that. I've already asked the question I will do again, but too long time ago and now we are in a completelly different circunstance here. The question is about the polarization model of gromacs: is it intended to include other models, like dipole moments interaction (like thole's one) or fluctuating charges in gromacs 4.0, in addition to the current charge on spring one? Long time ago, when I made such a question, the reason was no. I'm sorry for asking it again now, and I feel I should explain my reasons: I'm (finally) finishing my PhD now, and will probably give a try for a pos-PhD. Maybe one of but probably the most exciting possibility at moment for its project would be an extension of the current force-fields I've been developing and validating (soon to be published) with a polarization potential. IF everything goes ok, we would like to give a try to other potentials, like the ones mentioned, before choosing the best one for the types of systems we usually work with. That's basically the reason why I made such a question: if gromacs 4.0 is going to release with this potentials as options, it would be fairly easy and straight forward. If not, but there is any movement inside the developers section, I would join it right now just to see how thing are going (unfortunatelly, it would be impossible to begin to participate in such a project right now, exactly because the finalization of the PhD). If there is no movement for that, I would join only with 4.0 released and my free time back if I get my appliance accept, in order to learn a bit more about gromacs development and try to do this slice of the job by myself. ;) Thanks a lot for your time, and please forgive me again for my intrusion. ;) Sincerally yours, Jones On 6/23/07, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi Mark. Haven't got exactly what you said. So let me rephrase myself: The CF4 molecule doesn't have dihedrals nor intramolecular LJ and coulombic contributions. What kind of contribution am I missing that makes potential energy minus bond stretching minus angle bending *different* from Lj + coulomb(SR) + coulomb (LR) + Disp correction? Thanks a lot in advance, Sincerally yours, Jones I didn't follow the whole discussion, but there are also exclusion corrections when using PME or RF. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] New single thread performance numbers
Hi Erik. Still under NDA? Haven't it been lift last sunday? Anyway: I don't know exactly the terms of the NDA, So if you can't answer me the following question, please say no, I can't answer. I'm in touch with people having some compability issues with their Barcellonas and MBs, so could you tell us what are the configs you are dealing with? If that information is also under the NDA, really sorry for the question. Sincerally yours, Jones On 9/17/07, Erik Lindahl [EMAIL PROTECTED] wrote: Hi, Yes, the SPEC numbers aren't representative for typical gromacs performance. Technically I'm still on NDA for the benchmarks I ran on Barcelona so I can't share the exact numbers with you, but on average the performance will be pretty much the same _per_clock_ as Intel Clovertown. AMD scales a little bit better, but Intel benefits from a larger cache. Still, it's very nice to see that AMD is at least back on the field again. Let's hope for an aggressive frequency ramp-up and a price war ;-) Cheers, Erik On Sep 17, 2007, at 2:58 PM, Mark Abraham wrote: Florian Haberl wrote: Hi, Barcelona is out now and SPEC CPU2006 (www.spec.org) has released new numbers (I have taken them from the german c't magazin www.heise.de): Single core performance: 435.gromacs Opteron 2350 74.4 Opteron 51.1 Xeon X5365 143.3 Caveat that these numbers are for simulations without assembly optimization - i.e. C nonbonded loops. The assembly ones are considerably faster. Ref - GROMACS website. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to Install GMX V3.3.1 with Intel fortran compiler?
Hi. Yes, but that is the gcc solution. No prblem with those, except for giving away the challenge to make it work with intel compilers. Basically: I couldn't find a way much better. The way I trid in the time I tried, included compilation of the loops and only the loops using gcc to make the assembly works... :P Sad, the computer won that on me... :P Wish you have better luck! :) Jones On 9/13/07, Erik Lindahl [EMAIL PROTECTED] wrote: Hi, Well, I have a much simpler solution - there is no reason whatsoever to use fortran on ia32 or x86-64 since Gromacs will always use the much faster SSE assembly loops. Cheers, Erik On Sep 13, 2007, at 8:44 AM, Diego Enry wrote: This works for me: % vim /etc/ld.conf /opt/intel/mkl/8.0/lib/em64t/ = only if you have installed MKL /opt/intel/fce/9.0/lib/ /opt/intel/cce/9.0/lib/ then run % ldconfig If you wish, you may also add the 32bit libs: /opt/intel/mkl/8.0/lib/32/ = only if you have installed MKL /opt/intel/fc/9.0/lib/ /opt/intel/cc/9.0/lib/ On 9/13/07, liu xin [EMAIL PROTECTED] wrote: Dear GMX-users: I've searched the list but couldnt find something usful for me, and this is how I did it so far : source /opt/intel/fce/version/bin/ifortvars.sh export F77=ifort export CPPFLAGS=-I/home/xin/programs/fftw312/include export LDFLAGS=-L/home/dong/programs/fftw312/lib configure --prefix=/home/xin/programs/gromacs331 --enable-fortran --enable-mpi make mdrun make install-mdrun after the installation, I tried to do the mdrun: mpirun -np 2 /home/xin/programs/gromacs331/mdrun -s ... and then I got the following error message: error while loading shared libraries: libsvml.so: cannot open shared object file: No such file or directory The OS of my pc is SUSE 9.3. And I found that the missing file, libsvml.so, was in /opt/intel/fce/version/lib Is there something wrong with my steps? or shoould I add some FFLAGS? I am not very familiar with fortran and Linux, any suggestions will be appreciated! Xin Liu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular Universidade Federal do Rio de Janeiro - Brasil. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Ionic liquids
Hi. I would not agree with the fact that the approach isn't good. The dialkylimidazolium cation class has a lot of interest on it, which leaded to the development of force field for them rather than others. It doesn't mean that there isn't force field for the [EtNH3]+ [NO3]- IL, but means that there is no obvious reason for someone avoid those ions at a first glance. But, in fact, one should avoid the chlorine as counter-ion because it leads to ILs with a slight larger melting point. There are better options. On the other hand, a lot depends on the literature. I would expect that there would be more studies for the interaction of enzimes with dialkylimidazolium cation based ILs than any other class. BUT, I can be deadly wrong on this point. Back to the beggining: having 10 thousand water molecules, with 3 atoms only and usually rigid, is much simpler than 10 thousand cations with about 25 atoms in a fully flexible structure, in a box which *must* have the same number of countercharges, with anions of at least 5 atoms (which can sometimes be made rigid). The computational cost of such a simulation would rise in a amazingly way when compared to usual aqueous simulations. Best regards and good luck! Sincerally yours, Jones On 8/22/07, SeungPyo Hong [EMAIL PROTECTED] wrote: Sorry for late respond~ I totally agree with you. Frankly, I don't have any idea about that kind of idea. I just help the guy to do what he want to do. Anyhow, as Mark said, I think some experiment is required to get a meaningful result. First I warn you that this is not a good approach at all. He want to simulate [EtNH3]+ [NO3]-. I think that the structure of the is relatively simple and thus made their structure with WebMO(Gaussian). Then to get the groamcs topology, I use PRODRG server. The partial charge of them are corrected to same as Gaussian result. Then I placed them in a lattice with a same interval. And run MD simulation with only solvent. By doing this I can get a solvent coordinate in a box. Using this solvent coordinate and topology, you can run MD. But PRODRG does not give an accurate information and thus be careful. Good luck On 8/16/07, Sampo Karkola [EMAIL PROTECTED] wrote: Hi, nice to hear that someone else is also interested in doing MD in room temperature ionic liquids. What kind of ions do you use? Bmim chlorides perhaps, or do you have a larger counterion to bmim? Or a completely different cation? As Mark pointed out, if you do not have a properly parameterised force field for ILs, the results probably are not reliable, but I still would like to hear how did you define the parameters and how the mdruns performed. Regards, Sampo __ Sampo Karkola Doctoral student Laboratory of Organic Chemistry Department of Chemistry POBox 55, FIN-00014 University of Helsinki Finland tel. +358 9 19150369 fax. +358 9 19150366 [EMAIL PROTECTED] SeungPyo Hong wrote: On 8/16/07, *Mark Abraham* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Sampo Karkola wrote: Dear all, I was wondering if there are any parameters defined for ionic liquids? Some enzymes have retained their activity when the solvent has been a mixture of water and ionic liquids and it would be interesting to study the actual catalytical reactions in such a solvent. I don't know how you can mix an ionic liquid and water and not get a really hot aqueous solution that would smash an enzyme :-) I'm not an expert on the ionic liquids field or in simulating reactions, but ionic liquids have been used in eg. microwave-assisted synthesis with promising results. If one wants to study the reactions that take place in ionic liquids, with or without an enzyme catalysing it, are there any well-known procedures to follow? Is Gromacs the correct tool for that? I'm not going to study such reactions, at least not at the moment, but I'd just like to know how/if they can be done. If you distort the solvent too far from pure water, the parameterization process of these force fields will no longer be valid for studying the systems you want. Parameterizing new force fields for these solvents is probably not a worthwhile undertaking, and definitely not one to do lightly. Mark ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]
[gmx-users] PME or SPME?
Hi all. Well, I have some kind of a didatic doubt: Ok, from what I can understand up to now, PME uses lagrande interpolation for the genaration of the grid, while SPME uses cardinal B-splines to do so. Is it correct? And if, so, gromacs implements PME or SPME (the manual states PME, but also states B-splines)? Thanks a lot in advance! Jones ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Ionic liquid parameters
Hi people. Well, this thread is going to become an independet list for ILs. We have developed a force field for a small set of cations and anions of ILs, few year ago, based on AMBER. At the moment, we are (slowly) finalizing publications on the extension of those for new sets of anions, all compatible with the earlier methodology. Also, we are moving our simulations from the original code to gromacs, and right now we have some topologies in test. In case someone is interested: de Andrade J, Boes ES, Stassen H, J. Phys. Chem. B 106 (14): 3546-3548 APR 11 2002 de Andrade J, Boes ES, Stassen H, J. Phys. Chem. B 106 (51): 13344-13351 DEC 26 2002 de Andrade J, Boes ES, Stassen H, Abst. Pap. Am Chem. Soc. 226: U618-U618 022-IEC Part 1, SEP 2003 de Andrade J, Boes ES, Stassen H, Ionic Liquids IIIA: Fundamentals, Progress, Challenges, and Opportunities, Properties and Structure ACS Symposium Series 901: 118-133 2005 By the way: simulating an IL solvationg an enzime can be quite a challenge: ILs simulation boxes shall never be too small due to the electrostatics, and all will dependes on the enzime size so. But it will be amazing interesting and should be tried. :) With the best regards, Jones On 8/16/07, Sampo Karkola [EMAIL PROTECTED] wrote: Hi, thanks for the info! I also found a force field for AMBER. J. N. Canongia Lopes, J. Deschamps, A. A. H. P$dua, J. Phys. Chem. B. 2004, 108, 2038 –2047. Sampo [EMAIL PROTECTED] wrote: Dear gmx users. I see that are people in the list asking for ionic liquids parameters. I have been working on ionic liquids and I recently published the parameterization of two ionic liquids ([BMIM][PF6] and [BMIM][NO3]) for the gromos force field using gromacs. The parameters are published in: Micaelo, N.M., Baptista, A.M., Soares, C.M. (2006) Parameterization of 1-Butyl-3-Methylimidazolium Hexafluorophosphate/Nitrate Ionic Liquid for the GROMOS force field, J.Phys.Chem.B, 110, 1-14451. Have fun. Nuno Micaelo E-mail: [EMAIL PROTECTED] www: www.itqb.unl.pt/~micaelo/ Phone: (351)214469611 Fax: (351)214411277 Instituto de Tecnologia Química e Biológica Protein Modeling Group Apartado 127 2781-901 Oeiras Portugal º¤ø,¸,ø¤º*`*º¤ø,¸¸,ø¤º*`*º¤ø,¸¸,ø¤º*`º¤ø,¸,ø ,ø¤º*`*º¤ø,¸¸,ø¤º*`*º¤ø,¸¸,ø¤º*`*º¤ø,,ø¤º*`* ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to remove an energy contribution in gromacs?
Hi all. Well, I'm trying to calculate an E energy from my simulations, where E here stands only for the sum of *intermolecular* vdw and coulombic terms, and LJ(1-4) and coul(1-4). This means that I should find a way to exclude any 1-5, 1-6, 1-7 and so on contributions for coulombic and vdw energies, which I guess are included in the SR terms if the rcut is long enough. I though on doing it by use of a modified topology (with an arbitrary increased nexcl term) after the simulation is completed just for a -rerun job, and then use the g_energy program to calculate these contributions. Unfortunatelly, for some reason I'm not getting the correct values by large differences. Properly saying, only doing the above described procedure is yelding me even modifications in the bond, angle and dihedral terms of my simulations, which should not vary in a rerun with new nexcl values. Moreover, all energy terms with no exception seem to be only divided by a factor around 10., in comparison with the simulations with the original nexcl. I'm pretty sure I'm missing something here, but I have no idea of what could it be. Could someone please help me with this matter somehow? Thanks a lot in advance. Sincerally yours, Jones ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to remove an energy contribution in gromacs?
Hi Mark. Thanks a lot, first of all. ;) Unfortunatelly, the suggestion will not work: as you mentioned, there is a limit for 256 molecules, and my systems are composed by at least 500. Moreover, I still don't see any reason why the nexcl could affect the bond, angle nd dihedrals energy outputs. :( Any other thoughts? Thanks a lot, Jones On 8/6/07, Mark Abraham [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi all. Well, I'm trying to calculate an E energy from my simulations, where E here stands only for the sum of *intermolecular* vdw and coulombic terms, and LJ(1-4) and coul(1-4). This means that I should find a way to exclude any 1-5, 1-6, 1-7 and so on contributions for coulombic and vdw energies, which I guess are included in the SR terms if the rcut is long enough. If you define each molecule as an energy group, then GROMACS will report all the self vdW and Coulomb terms, and all pairwise terms and you can add up whatever ones you want. This won't work if you have more than 256 molecules, though. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to remove an energy contribution in gromacs?
Hi both. @ Mark: thanks mark. Have to admit that I haven't thought about the exclusions possibility. Specially because I was looking for a simple way of doing it without removing the dynamics related to these forces from the simulation itself. So, changing the nexcl looked a bit easier to do. @ Berk: This seems the right approach to me. I don't know what you are doing exactly. But are you aware that the averages in g_energy and in the log file are using every integration step, whereas with rerun you only get values for every frame in your trajectory? I think the averages of mdrun -rerun are still incorrect, you need to use the average of the values in the energy.xvg file. Ok, let me see if I understood: This means that, if I simulated originally with the .mdp saying for the system to save the trajectory every 10 time steps, and even with this fact still mentioned in the .mdp file for the mdrun -rerun job, it would barelly mean that the energies would be divided by a factor of 10, and the oscilations are due to the reduction in the statistics? Is it correct? So, the proper way of doing if is not just keep on saying on the .mdp file that it's saved every 10 time steps, but rather more or I just get the results and multiply them by 10, or make the rerun informing a 10 times larger time-step? Also obtaining accurate potential energy averages for even small systems requires a LOT of statistics. I know it. It's just the first runs (only 200k steps of simulation, 20k steps saved), and the results will guide me towards the proper acquisition time. ;) Thanks a lot you both for the help in advance. Sincerally yours, Jones ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to remove an energy contribution in gromacs?
@Xavier: So, this means: nstxtcout from 10 to 1 nsteps from 10 to 1 nstlog from 10 to 1 nstenergy from 10 to 1 nstlist from 5 to 1. This is what should be changed in the .mdp file in order to get a proper rerun g_energy analysis? @Berk: Thanks a lot for the clarification. But still could not understand why there is any need for using g_analyze. Could you ple clarify this point out for me? Thanks a lot for everybody in advance! Jones On 8/6/07, Xavier Periole [EMAIL PROTECTED] wrote: You should also update your neighbor list every step (10ps). if you the original 5/10 steps frequency mdrun -rerun will update them every 5/10*10ps ... XAvier From: Jones de Andrade [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] how to remove an energy contribution in gromacs? Date: Mon, 6 Aug 2007 11:13:44 -0300 Hi both. @ Mark: thanks mark. Have to admit that I haven't thought about the exclusions possibility. Specially because I was looking for a simple way of doing it without removing the dynamics related to these forces from the simulation itself. So, changing the nexcl looked a bit easier to do. @ Berk: This seems the right approach to me. I don't know what you are doing exactly. But are you aware that the averages in g_energy and in the log file are using every integration step, whereas with rerun you only get values for every frame in your trajectory? I think the averages of mdrun -rerun are still incorrect, you need to use the average of the values in the energy.xvg file. Ok, let me see if I understood: This means that, if I simulated originally with the .mdp saying for the system to save the trajectory every 10 time steps, and even with this fact still mentioned in the .mdp file for the mdrun -rerun job, it would barelly mean that the energies would be divided by a factor of 10, and the oscilations are due to the reduction in the statistics? Is it correct? Yes. The factor will not be exactly 10 though, since there are some end effects. With may frames it will be very close to 10 though. So, the proper way of doing if is not just keep on saying on the .mdp file that it's saved every 10 time steps, but rather more or I just get the results and multiply them by 10, or make the rerun informing a 10 times larger time-step? You can not fix the problems caused by this bug. For the average values of the rerun you should just run g_energy and extract the average from the energy.xvg file using for instance g_analyze. Berk. _ Hotmail en Messenger on the move http://www.msn.nl/services ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - XAvier Periole - PhD 1- Institute of Molecular Assemblies City University of New York - USA 2- Molecular Dynamics-Group University of Groningen - The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mdrun -rerun + runedr: combo problem?
Hi all. I think I'm having a really strange problem: Well, I have some simulations being performed, and wanted to remove from the bigger molecules any vdw or coulombic intramolecular interaction longer than 1-4. So, from 1-5 included forward, I would like to remove from the energetic calculations, but not from the interaction dynamics. To do so, I've performed the simulation with nexcl = 3 (standard, and which would include them in the dynamics), and after I increased this number and performed a mdrun -rerun ressimulation. Then, I runned the runedr. The problem is: I decided to make a test run. I expect that a nexcl number bigger than the total should not yeld problems. So I choosen to increase the nexcl in C2F6 from the standard 3 to 4. Then I runned runedr in both results, and got the following: nexcl = 3: Energy Average RMSD Fluct. Drift Tot-Drift --- Bond3040.6970.069766.5161 0.381591 76.3189 Angle 4220.7279.105778.0402 -0.224121 - 44.8247 Ryckaert-Bell. 22594.3 0.369332 0.369284 0.000103437 0.0206876 LJ-14 4345.4744.791144.5899 -0.0734496 - 14.6901 Coulomb-14 26656.312.583112.5831 0.000785301 0.157062 LJ (SR)-7476.6169.867869.7072 -0.0820061 - 16.4014 Disper. corr. -233.0131.803321.80306 -0.000532475 - 0.106496 Coulomb (SR)202.0883.639033.62648 -0.00522946- 1.0459 Coul. recip. -228.367 1.41591.40872 0.00246637 0.49328 nexcl = 4: Energy Average RMSD Fluct. Drift Tot-Drift --- Bond312.923891.374891.099 0.383169 76.6345 Angle 425.5231210.881210.81 -0.224334 - 44.8673 Ryckaert-Bell. 2259.646430.136430.13 8.98693e-05 0.017974 LJ-14 434.6821236.91 1236.9 -0.073917 - 14.7835 Coulomb-14 2665.877586.127586.12 0.000608334 0.121668 LJ (SR)-747.6912127.892127.89 -0.0822151 - 16.4432 Disper. corr. -23.303466.315766.3157 -0.000532475 - 0.106496 Coulomb (SR)20.210557.510857.5101 -0.00521119 - 1.04225 Coul. recip. -22.838764.988864.9886 0.00246332 0.492669 And the results, for me, doen't make sense. First, all the contributions, *including* bonds, angles and dihedralss that are *not* to be affected by the nexcl, are reduced by almost 10. Second, since we are talking about C2F6, which doesn't have any atom farthen than 3 bonds from any other, neither the vdw and coulombic contibutions should have been affected. Could please someone help me with this matter? What have I missed in the logics here? Thanks a lot for everybody in advance! Sincerally yours, Jones ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] More dihedral doubts
Hi all again. Sorry for bothering all you with this dihedrals subject. Well, I'm trying this in my .itp file: ** [ dihedraltypes ] ; i j k l functphi (degree) cp (kJ/mol.rad^2) mult(n) CTCTNTCT1 0.00 1.25520 3.0 ;amber99 CTCTNTCT1180.00 2.00832 2.0 ;amber99 X CTNTX 1 0.00 1.25520 3.0 ;amber99 ;padrao CTCTCTCT1 0.00 0.75312 3.0 ;amber99 CTCTCTCT1180.00 1.04600 2.0 ;amber99 CTCTCTCT1180.00 0.83680 1.0 ;amber99 F CTCTF 1 0.00 0. 3.0 ;amber99 F CTCTF 1180.00 5.20800 1.0 ;amber99 X CTCTX 1 0.00 0.6530 3.0 ;amber original e 99 ;padrao But I just found that grompp is yelding this for me: ** processing topology... WARNING 1 [file ../top/ff_amber_perF.itp, line 62]: Overriding Proper Dih. parameters, old: 0 1.2552 3 0 0 0 new: CT CT NT CT 1 180.00 2.00832 2.0 WARNING 2 [file ../top/ff_amber_perF.itp, line 65]: Overriding Proper Dih. parameters, old: 0 0.75312 3 0 0 0 new: CT CT CT CT 1 180.00 1.04600 2.0 WARNING 3 [file ../top/ff_amber_perF.itp, line 66]: Overriding Proper Dih. parameters, old: 180 1.046 2 0 0 0 new: CT CT CT CT 1 180.00 0.83680 1.0 WARNING 4 [file ../top/ff_amber_perF.itp, line 68]: Overriding Proper Dih. parameters, old: 0 0 3 0 0 0 new: F CT CT F 1 180.00 5.20800 1.0 *** What does it mean? What kind of mistake am I doing? Am I wrong, or definitelly gromacs still doesn't support multiple trigonometric dihedral potentials and then I really need to transform it on a RB-potential (and the reference I found on a web site is wrong)? Thanks a lot in advance... Any help would be really welcome. :) Sincerally yours, Jones ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Help with RB dihedrals implementation
Hi all. Well, I just tried something different, and it worked. Found on the net that the 3.3.1 version of gromacs allows me to use sum of different periodic potential for the same dihedral, making it unecessary to use RBs. So, if I write the dihedrals in the form: F CTCTF 1 0.00 0. 3.0 F CTCTF 1180.00 5.20800 1.0 X CTCTX 1 0.00 0.6530 3.0 The first two potential will sum up together to describe the dihedral of F-CT-CT-F, while all other dihecrals centered in a bond CT-CT will be defined by the potential described in the fourth line, correct? If anyone could confirm or deny it for me that would be really helpfull. Thanks a lot in advance for everything. Jones On 7/27/07, Mark Abraham [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi Mark. Thanks a lot. I'm already trying to find some clue in the manual. Anyway, what sort of extra information could be usefull? Not off the top of my head. Please post your .top file, and the section of the .itp file you've modified, including its [ header ]. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] dihedral doubts, again
Hi all. Well, I'm having a few problems in implementing an opls-like dihedral potential, what mean, a serie of different periodic dihedral potentials. After much problem with the RB potential conversion, Ifound on the net that the 3.3.1 version of gromacs allows me to use sum of different periodic potential for the same dihedral, making it unecessary to use RBs. So, if I wrote the dihedrals in the form: F CTCTF 1 0.00 0. 3.0 F CTCTF 1180.00 5.20800 1.0 X CTCTX 1 0.00 0.6530 3.0 And grompp at least swallowed it. But I'm not quite sure if I understand how is he dealing with it. From what I understand, the first two potential will sum up together to describe the dihedral of F-CT-CT-F. Then, all other dihedrals centered in a bond CT-CT and that haven't been explicit defined before will be defined by the potential described in the fourth line, correct? If anyone could please clarify this matter better for me I would be very thankfull. Thanks a lot in advance for anything. Jones ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Help with RB dihedrals implementation
Hi Mark. Thanks a lot. I'm already trying to find some clue in the manual. Anyway, what sort of extra information could be usefull? Thanks a lot again! ;) Jones On 7/26/07, Mark Abraham [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi all. I'm trying to implement a samll RB-potential for some molecules I'm working with. I choosen to go following the files from opls-aa force field included with gromacs. Unfortunatelly, I get this error: No default Proper Dih. types, using zeroes Which is quite strange, as the error latelly refers to the following lines: CT CT CT F 3 0.65084 1.95253 0.0-2.60338 0.0 0.0 F CT CT F 3 5.02080 5.02080 0.0 0.0 0.0 0.0 And, for a final point that makes my doubt, I don't see any difference between this lines and this ones from ffoplsaabon.itp from gromacs 3.3.1 itself: CA CT CT NC 3 5.77183 -2.67148 0.95814 -4.05848 0.0 0.0 ; CA CT CT NT 3 3.33465 -1.55226 2.82001 -4.602400.0 0.0 Could anyone give me some help on this issue, please? I guess that you've mangled some format, either in your modifications to the .itp file or your .top file. Read the relevant parts of Chapter 5 closely and compare with what you've done. We can't tell what the problem is from the information you've provided so far. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Help with RB dihedrals implementation
Hi all. I'm trying to implement a samll RB-potential for some molecules I'm working with. I choosen to go following the files from opls-aa force field included with gromacs. Unfortunatelly, I get this error: No default Proper Dih. types, using zeroes Which is quite strange, as the error latelly refers to the following lines: CT CT CT F 3 0.65084 1.95253 0.0-2.60338 0.0 0.0 F CT CT F 3 5.02080 5.02080 0.0 0.0 0.0 0.0 And, for a final point that makes my doubt, I don't see any difference between this lines and this ones from ffoplsaabon.itp from gromacs 3.3.1itself: CA CT CT NC 3 5.77183 -2.67148 0.95814 -4.05848 0.0 0.0 ; CA CT CT NT 3 3.33465 -1.55226 2.82001 -4.60240 0.0 0.0 Could anyone give me some help on this issue, please? Thanks a lot to everybody in advance. Sincerally yours, Jones On 7/19/07, George Abadir [EMAIL PROTECTED] wrote: Yes of course I looked at the output but I thought is I specify energy groups it will output only those specified and not the whole system. However I tried a short run and it did output both. For the crash it turned out it is because all the nodes try to read the huge trajectory file at the same time if this may help somebody in the future. We are still trying to figure out how to solve this problem anyway. Thanks for your time. George Mark Abraham wrote: George Abadir wrote: Hi all, I am running simulations of carbon nanotubes and amino acids in water. I need to calculate the potential energies for the whole system as well as the interaction energy between the CNT and amino acid. What I am tried to do is to calculate the energy for the whole system first (i.e. I did not introduce any energygrps in the run.mdp file) and then use the rerun option to calculate the interaction energy after introducing energygrps= CNT Protein SOL into the run.mdp file. However, each time I try to run this second step the cluster on which I run the simulation crashes with a message Kernel panicked! Does any body know about this problem? Yeah, something's broken that's probably got nothing to do with GROMACS, or the fact you're doing a re-run. Is there another way to get both the potential energy of the system as well as the interaction potential energy? I understand that if I write energygrps= CNT Protein SOL from the very beginning the energy of the whole system won't be written, is that right? mdrun always calculates the total potential and kinetic energy, and outputs it according to nstxxx flags. Have you not looked at typical output, or typical .edr file contents? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Buckingham Potential Doubt.
Hi all. I was just wondering, and I even think this is a stupid question: As well as there are the Lorentz-Berthelot combination rules (among others) for the sigma and epsilon from Lennard-Jones parameters of different atom types, how can the parameters from Buckingham potential of different atom types be combined? Thanks a lot in advance, Jones ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] intermolecular energy
Hi Mark. Haven't got exactly what you said. So let me rephrase myself: The CF4 molecule doesn't have dihedrals nor intramolecular LJ and coulombic contributions. What kind of contribution am I missing that makes potential energy minus bond stretching minus angle bending *different* from Lj + coulomb(SR) + coulomb (LR) + Disp correction? Thanks a lot in advance, Sincerally yours, Jones On 6/23/07, Mark Abraham [EMAIL PROTECTED] wrote: The intermolecular energy in the liquid should no be equal to the sum of the LJ, coulomb(SR, coulb(LR) and Disp Correction? And, that correct, shouldn't it be equal also to the potential energy minus bond minus angle bending energies? What am I missing, that is making me have both different? Dunno since we can't read your mind about the sort of calculation you did... What does your logfile have? Another question: what exactly is the coul. recip. standing for? I expected it had to be included in the above sums also, but the high values it yelds would be nonsense. It's the reciprocal space sum of the Ewald method you're using. It sounds like you should read the section in chapter 4(?) of the manual that describes this. The reason it's large is that it has (roughly) all the long-range contributions from all of the atoms, and I don't think these can be sensibly broken down into by-atom components. So if you're interested in determining intermolecular energies, for some reason, you should design a simulation protocol that has a chance of doing this. In a GROMACS context, that probably means GRF electrostatics. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] intermolecular energy
Hi David! Ha, so there is something extra? Thanks a lot :) I knew I was forgeting something. So how should I deal with it? I mean, what are the contibutions that are inside the Potential option of g_energy? Does it include all corrections, disp.corr. ones also, or there is something missing? Thanks a lot! Jones On 6/23/07, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi Mark. Haven't got exactly what you said. So let me rephrase myself: The CF4 molecule doesn't have dihedrals nor intramolecular LJ and coulombic contributions. What kind of contribution am I missing that makes potential energy minus bond stretching minus angle bending *different* from Lj + coulomb(SR) + coulomb (LR) + Disp correction? Thanks a lot in advance, Sincerally yours, Jones I didn't follow the whole discussion, but there are also exclusion corrections when using PME or RF. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] intermolecular energy
Hi David. Just tried it, and it isn't getting not even funny! Ok, without using the nmol flag, calculated total, potential and kinetic energy. Results: Potential -5109.4669.1951 68.569 0.128686 32.1718 Kinetic En. 3838.2167.941767.9418 -9.04753e-05 - 0.022619 Total Energy -1271.2596.784496.3384 0.128594 32.1488 As all can see: The total energy doesn't appear from the simple sum of kinetic and potential. I'm not expecting this to be a bug. But I'm not quite getting what am I forgeting. What kind of contribution can be lacking where? Thanks a lot in advance, Sincerally yours, Jones On 6/23/07, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi David! Ha, so there is something extra? Thanks a lot :) I knew I was forgeting something. So how should I deal with it? I mean, what are the contibutions that are inside the Potential option of g_energy? Does it include all corrections, disp.corr. ones also, or there is something missing? these are inside the Coulomb LR (PME) or some other Coulomb term (RF corrections). Energy is of course the sum of all terms. Try without the nmol flag to g_energy first. Thanks a lot! Jones On 6/23/07, *David van der Spoel* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi Mark. Haven't got exactly what you said. So let me rephrase myself: The CF4 molecule doesn't have dihedrals nor intramolecular LJ and coulombic contributions. What kind of contribution am I missing that makes potential energy minus bond stretching minus angle bending *different* from Lj + coulomb(SR) + coulomb (LR) + Disp correction? Thanks a lot in advance, Sincerally yours, Jones I didn't follow the whole discussion, but there are also exclusion corrections when using PME or RF. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED][EMAIL PROTECTED] mailto:[EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] intermolecular energy
Hi all. First, I would like to apologize for the previous message. Maybe I've been too harsh? Sorry for that. Second, I would like to list all the energetic contributions for one (same system, different run) run that g_energy allowed me to get: Energy Average RMSD Fluct. Drift Tot-Drift --- Bond2.05116 0.0591887 0 -0.123751 - 30.9381 Angle 2.638 0.0664036 0 0.114896 28.7242 LJ (SR)-14.3726 0.0865671 0 -0.0877988 - 21.9499 Disper. corr. -0.378693 0.00211843 0 -0.00185533 - 0.463837 Coulomb (SR) 0.128875 0.0164563 0 0.000956545 0.239138 Coulomb (LR) 0.00237452 4.3944e-05 0 3.95014e-05 0.00987542 Coul. recip. -145.145 0.660423 0.652976 -0.00137031 - 0.34258 Potential -10.2211 0.138681 0 -0.0988822 - 24.7207 Kinetic En. 7.67642 0.0990863 0.0988019 0.000103943 0.025986 Total Energy -2.54473 0.167497 0 -0.0987789 - 24.6949 Temperature 123.15 1.5896 1.5896 3.34002e-06 0.000835011 Ok, those are with nmol 500, but it doesn't seem to matter that much. If anybody asks, I can do all them again without that. Any help would be really thankfull! Sincerally yours, Jones On 6/23/07, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi David! Ha, so there is something extra? Thanks a lot :) I knew I was forgeting something. So how should I deal with it? I mean, what are the contibutions that are inside the Potential option of g_energy? Does it include all corrections, disp.corr. ones also, or there is something missing? these are inside the Coulomb LR (PME) or some other Coulomb term (RF corrections). Energy is of course the sum of all terms. Try without the nmol flag to g_energy first. Thanks a lot! Jones On 6/23/07, *David van der Spoel* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi Mark. Haven't got exactly what you said. So let me rephrase myself: The CF4 molecule doesn't have dihedrals nor intramolecular LJ and coulombic contributions. What kind of contribution am I missing that makes potential energy minus bond stretching minus angle bending *different* from Lj + coulomb(SR) + coulomb (LR) + Disp correction? Thanks a lot in advance, Sincerally yours, Jones I didn't follow the whole discussion, but there are also exclusion corrections when using PME or RF. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED][EMAIL PROTECTED] mailto:[EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org
Re: [gmx-users] intermolecular energy
Hi David. Well, as long as I can remember, I pushed the last gromacs sources at time ( 3.3.1) and just installed it. Anyway, mdrun tells me it is 3.3 and g_energy says it is 3.2.1 (in the run headers). I expected this to be normal, or could I have run in some kind of unnexpected or unremembered problem? About coul.recip.: Those results above, of the big list, all include -nmol 500. It means that coul. recip. should be divided by 500² instead of only 500? About twin-range: only if I'm unaware of it. In order to be sure, I'm pasting here the mdp file I'm using. But, as far as I know, the answer is no, I'm not using twin-range. Tnaks a lot in advance, Sincerally yours, Jones .mdp file follows: cpp = /lib/cpp integrator = md tinit = 3650.000 dt = 0.002 nsteps = 125000 nstcomm = 1 nstxout = 0 nstvout = 0 nstfout = 0 nstxtcout = 10; 5 ;10 xtc-precision = 1000 ;NAO MEXER! nstlog = 10 nstenergy = 10 nstlist = 5 energygrps = System ns_type = grid ; Constraints use is: constraints = none constraint_algorithm = lincs ;Treatment of Vdw and Elctrostatics: vdwtype = cut-off DispCorr= EnerPres rlist = 1.25 rvdw= 1.25 coulombtype = PME rcoulomb= 1.30 fourierspacing = 0.1 pme_order = 4 ewald_rtol = 1e-05 optimize_fft= yes ; Temperature coupling is: Tcoupl = nose-hoover tau_t = 0.030 tc-grps = System ref_t = 123.15 ; Pressure coupling is: Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 2.500 compressibility = 4.5e-5 ref_p = 1.01325 ;bar == 1. atm ; Generate velocites at 123K is: gen_vel = no gen_temp= 123.15 ;gen_seed= 173529 gen_seed= 12041979 On 6/23/07, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi all. First, I would like to apologize for the previous message. Maybe I've been too harsh? Sorry for that. Second, I would like to list all the energetic contributions for one (same system, different run) run that g_energy allowed me to get: Energy Average RMSD Fluct. Drift Tot-Drift --- Bond2.05116 0.0591887 0 - 0.123751 -30.9381 Angle 2.638 0.0664036 0 0.114896 28.7242 LJ (SR)-14.3726 0.0865671 0 -0.0877988 -21.9499 Disper. corr. -0.378693 0.00211843 0 -0.00185533 -0.463837 Coulomb (SR) 0.128875 0.0164563 0 0.000956545 0.239138 Coulomb (LR) 0.00237452 4.3944e-05 0 3.95014e-05 0.00987542 Coul. recip. - 145.145 0.660423 0.652976 -0.00137031 -0.34258 Potential -10.2211 0.138681 0 -0.0988822 -24.7207 Kinetic En. 7.67642 0.0990863 0.0988019 0.000103943 0.025986 Total Energy -2.54473 0.167497 0 -0.0987789 -24.6949 Temperature 123.15 1.5896 1.5896 3.34002e-06 0.000835011 Do you use an old version of g_energy with a newer mdrun? -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] intermolecular energy
Hi David. Thanks a lot. Just trying it now. The mistake of the g_energy was something I sould have expected: I use an old Suse version, which *has* gromacs 3.2 installed by standard. The paths where getting that one instyead of my actual one. I completelly forget that, specially cause for no reason the paths don't work, yast doesn't uninstall it and have to make use of the alias to get things working properly Next linux installation I do it in a cleaner way. ;) About the twin range, I'm rerunning to correct it. I've really didn't notice that when I choose the simulatins parameters of this whole series a long time ago. Really thank you very much. I'll post again after I get the new results to let be in the list if it is correct now or still has something wrong. May help others. Thanks a lot! Sincerally yours, Jones On 6/23/07, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi David. Well, as long as I can remember, I pushed the last gromacs sources at time (3.3.1) and just installed it. Anyway, mdrun tells me it is 3.3 and g_energy says it is 3.2.1 (in the run headers). I expected this to be normal, or could I have run in some kind of unnexpected or unremembered problem? So that explains it: g_energy uses the names of the energy terms, and this exactly changed between 3.2 and 3.3. Hence Coul. Recip is not recognized as an energy term by the old g_energy. By the way you have rcoulomb rlist, there you are using twin range cut-off. You probably want to make them identical. Now you are computing the energies for particles at distance between 1.25 and 1.30 only every nstlist steps, while you are computing the energies for particles at Rij = 1.25 and particles at Rij= 1.30 at every step. About coul.recip.: Those results above, of the big list, all include -nmol 500. It means that coul. recip. should be divided by 500² instead of only 500? About twin-range: only if I'm unaware of it. In order to be sure, I'm pasting here the mdp file I'm using. But, as far as I know, the answer is no, I'm not using twin-range. Tnaks a lot in advance, Sincerally yours, Jones .mdp file follows: cpp = /lib/cpp integrator = md tinit = 3650.000 dt = 0.002 nsteps = 125000 nstcomm = 1 nstxout = 0 nstvout = 0 nstfout = 0 nstxtcout = 10; 5 ;10 xtc-precision = 1000 ;NAO MEXER! nstlog = 10 nstenergy = 10 nstlist = 5 energygrps = System ns_type = grid ; Constraints use is: constraints = none constraint_algorithm = lincs ;Treatment of Vdw and Elctrostatics: vdwtype = cut-off DispCorr= EnerPres rlist = 1.25 rvdw= 1.25 coulombtype = PME rcoulomb= 1.30 fourierspacing = 0.1 pme_order = 4 ewald_rtol = 1e-05 optimize_fft= yes ; Temperature coupling is: Tcoupl = nose-hoover tau_t = 0.030 tc-grps = System ref_t = 123.15 ; Pressure coupling is: Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 2.500 compressibility = 4.5e-5 ref_p = 1.01325 ;bar == 1. atm ; Generate velocites at 123K is: gen_vel = no gen_temp= 123.15 ;gen_seed= 173529 gen_seed= 12041979 On 6/23/07, *David van der Spoel* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi all. First, I would like to apologize for the previous message. Maybe I've been too harsh? Sorry for that. Second, I would like to list all the energetic contributions for one (same system, different run) run that g_energy allowed me to get: Energy Average RMSD Fluct. Drift Tot-Drift --- Bond2.05116 0.0591887 0 - 0.123751 -30.9381 Angle 2.638 0.0664036 0 0.114896 28.7242 LJ (SR)-14.3726 0.0865671 0 - 0.0877988 -21.9499 Disper. corr. -0.378693 0.00211843 0 - 0.00185533 -0.463837 Coulomb (SR) 0.128875 0.0164563 0 0.000956545 0.239138 Coulomb (LR) 0.00237452 4.3944e-05 0 3.95014e-05 0.00987542 Coul. recip. - 145.145 0.660423 0.652976 -0.00137031 -0.34258 Potential -10.2211 0.138681 0 - 0.0988822 -24.7207 Kinetic En
[gmx-users] BFGS in NMA calculations?
Hi! I was just wondering: am I completelly wrong, or gromacs uses the BFGS hessian approximation in order to do normal mode analysis, rather than the real and painfull to analitically second derive potentials hessian? I'm wondering also if this approximation is as good for NMA as it is for minimization procedures. Thanks a lot in advance, Jones ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Polarizability
Hi David. I had no idea that gromos was using it. Also, just had a few clues that maybe charmm was. All amber clues however points towards a different model. I have a few concerns about directioning (really sure that this is the wrong word, if exists) that a shell model polarizability would make. Absolutely no doubts that it would be probably faster than any iterative model include dipoles, but I have this concern. I'll be looking forward for the charmm papers on it (I've found the references late this week) and try to compare its reproducibility and parametrization methodologies somehow. About implementing it: its a good idea, but a long term one. Basically it means that nobody in the developer's list seems to be working on it righ now, right? ;) Thanks a lot for all answers, David. :) Sincerally yours, Jones On 5/20/07, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi list. Well, a few days ago I've written a message concerning the future implementations that could be expected min gromacs 4 when it's released. Unfortunatelly, the thread hasn't gone any further. lots of plans, but no promises. we really don't want to raise any expectations, more than significantly increased performance both sequential and parallel. So, I would like to know if there is somone in this list who ever tried to modify gromacs program forces and energies routines. More specifically, if someone has tried to somehow implement any polarizability model in the force field, other than the shells model. no plans. the shell model will most likely be the dominant model, both gromos and charmm developers are using it now. if you feel like implementing other stuff yourself, you're welcome to continue the discussion on the developer list. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Polarizability
Hi list. Well, a few days ago I've written a message concerning the future implementations that could be expected min gromacs 4 when it's released. Unfortunatelly, the thread hasn't gone any further. So, I would like to know if there is somone in this list who ever tried to modify gromacs program forces and energies routines. More specifically, if someone has tried to somehow implement any polarizability model in the force field, other than the shells model. I'm deeply interested in it. Thanks a lot in advance, sincerally yours, Jones ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gromacs future development guidelines?
Hi Al.. Well, first of all sorry if this message becomes a bit out of the scope of the list. Since I've heard a lot of time ago somewhere in here that the gromacs 4.0was in development, today I remembered that and decided to ask google to give this a try. I basically found this 2 documents concerning it: http://xray.bmc.uu.se/hajdu/course_stuff/protein-folding.pdf https://extras.csc.fi/chem/courses/gmx2007/David_Talks/speeding.pdf Despite the wonderfull observation that with new gromacs plus huge computers or [EMAIL PROTECTED] approaches maybe folding will finally become real, I payed a lot of attention for the new implementations of the future gromacs's incarnations. Unfortunatelly, I could not find too much info on this (except, of course, for the exciting and promising REMD implementation). I would like to ask, if possible, what sort of new stuff is to be expected in the new and official version of gromacs, whenever it comes. My personal biggest curiosity are the simulation algorithms and force field potentials that can be choosen to be implemented in a near future. :) Hoping that this is not one of the questions I should not have asked... ;) Thanks for any answer in advance, Jones ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Compressibility issue - real concern
Hi all. Well, I'm having a great problem in some NpT simulations I'm running here, which leaded me to some concerns. Let me try to explain the situation: Ok, I know: everywhere, including this list, amber list and any computational chemistry list informs that the compressibility of the liquid doesn't really matters for the NpT simulations, it will just change the response time of the system. Knowing that, I've started to make some simulations on a new system here: CF4. NVT equilibration, box in the proper volume, 500 molecules. After long time, change to Parrinello-Rahman barostat. Almost blowed, but came back as fast as almost were lost. I was using tau_p of 0.400 and compressibility of 116 e-6 (not even I remember where that came from). The target volume is 45.66nm**3 at 123K and 1 atm. The potential is from AMBER, and is properly written in the topology files (reverified that about a thousand times). The system kept going to a average volume around 53.4 nm**3, didn't matter whatever I did with the simulation parameters. The reproducibility, from the original Kollman's paper, show's that there should be about 1-2% deviation. I kept trying for about 1ns of simulation, couldn't be more stable (it would be great if it was in the correct value!). After all reverifications possible, I decided to change exactly what is supposed to not alter this property: compressibility. I lowered it from 11.6e-5 to 4.5e-5. The volume reacted with an immediate drop to 50nm**3. I did not yet tried to change parrinello for berendsen. By now, I'm dealing with the tau_p increase, from 0.400 to 0.700, which also yelded me an reduction from 50nm**3 to 49-49.5nm**3. This means that it's not big deal to change the tau_p, what is also interesting since amber official and original guidelines uses the 0.400 ps coupling for pressure (only that with the nosè barosthat). The points I'm questioning here now is: 1 - Is the compressibility of the system a value that basically should not matter what I put in there? 2 - to what range is this not matter related? 3 - I'll keep trying the compressibility, and see if will reach at some value the expected volume. The question now is, will it reach any point acceptable? And after this point, will it be still stable, start to grow the volumes again, or will just keep falling (worst scenario)? 4 - since it should not affect the simulated property... what's happening here, in such a way that it IS affecting the simulated property? I'm really sorry if this is any kind of obvious subject, but I really tried to find any different reason for these observations. Could not find nothing related in any list, including this one. So I thought about taking the facts to the discussion list and see what appears. Thanks in advance for anyone and any answer! Sincerally yours, Jones ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Compressibility issue - real concern
Hi Berk! Thanks for your so fast answer! I'll try to look for a different tau_p. I would really feel 4 ps a too high value, even for water systems, but will look around before decision. Anyway, I'm still concerned about the compressibility value. Long time ago in this list I came to this question, and this is how this ended: *** Hi, ** ** Just use the water value for any liquid system (5e-5 or so). ** ** As the manual explains, it only affects the coupling time, not the ** equilibrium pressure. ** ** Cheers, ** ** Erik ** On May 3, 2006, at 8:54 PM, Jones de Andrade wrote: ** ** Hi all. ** ** Ok, this may sound like a stupid question, since the equations of the ** barostats clearly states the compressibility constant in it. ** ** But, in other programas I used to do NpT (usually with Nosè-Hoover) ** simulations, like DL_Poly and MDynaMix, I never had to input this ** parameter. Only reference pressure and pressure coupling time were ** needed. ** ** Does anybody here have a clue on it? Or, in a better way to ask: how ** can I make an NpT simulation, of a liquid with an unknown ** compressibility and which I maybe would like to estimate throw ** simulation, preferably without running in the error of inputing this ** as parameter? ** ** Thanks in advance. ** ** Jones* But, what's clear from the different simulation results with different compressibilities, is that the equilibrium density changes, since different input compressibilities yelds different average box volumes. I would expect them (tau_p and compressibility) working together in the coupling times, but not in the average volumes or densities. That's unnexpected, and gives me a bit of trouble, since I don't like to provide the simulation with extra information from the macroscopic world which I can later want to extract *from* the simulation. So, how can I deal with it? And, for certanly, should the compressibility affect the simulated system's volume or not? Thanks a lot in advance! Jones On 5/3/07, Berk Hess [EMAIL PROTECTED] wrote: From: Jones de Andrade [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: [gmx-users] Compressibility issue - real concern Date: Thu, 3 May 2007 06:33:12 -0300 Hi all. Well, I'm having a great problem in some NpT simulations I'm running here, which leaded me to some concerns. Let me try to explain the situation: Ok, I know: everywhere, including this list, amber list and any computational chemistry list informs that the compressibility of the liquid doesn't really matters for the NpT simulations, it will just change the response time of the system. Knowing that, I've started to make some simulations on a new system here: CF4. NVT equilibration, box in the proper volume, 500 molecules. After long time, change to Parrinello-Rahman barostat. Almost blowed, but came back as fast as almost were lost. I was using tau_p of 0.400 and compressibility of 116 e-6 (not even I remember where that came from). The target volume is 45.66nm**3 at 123K and 1 atm. The potential is from AMBER, and is properly written in the topology files (reverified that about a thousand times). The system kept going to a average volume around 53.4 nm**3, didn't matter whatever I did with the simulation parameters. The reproducibility, from the original Kollman's paper, show's that there should be about 1-2% deviation. I kept trying for about 1ns of simulation, couldn't be more stable (it would be great if it was in the correct value!). After all reverifications possible, I decided to change exactly what is supposed to not alter this property: compressibility. I lowered it from 11.6e-5 to 4.5e-5. The volume reacted with an immediate drop to 50nm**3. I did not yet tried to change parrinello for berendsen. By now, I'm dealing with the tau_p increase, from 0.400 to 0.700, which also yelded me an reduction from 50nm**3 to 49-49.5nm**3. This means that it's not big deal to change the tau_p, what is also interesting since amber official and original guidelines uses the 0.400 ps coupling for pressure (only that with the nosè barosthat). The points I'm questioning here now is: 1 - Is the compressibility of the system a value that basically should not matter what I put in there? 2 - to what range is this not matter related? 3 - I'll keep trying the compressibility, and see if will reach at some value the expected volume. The question now is, will it reach any point acceptable? And after this point, will it be still stable, start to grow the volumes again, or will just keep falling (worst scenario)? 4 - since it should not affect the simulated property... what's happening here, in such a way that it IS affecting the simulated property? I'm really sorry if this is any kind of obvious subject, but I really tried to find any different reason for these observations. Could not find nothing related in any list
Re: [gmx-users] Compressibility issue - real concern
Hi Erik. I was thinking something about it exactly now. I mean, Berk quoted that the scalling goes with beta/tau in Berendsen, and with beta/tay^2 in Parrinello. I mean, in a similar implementation, how should it go for a nosè implementation? Also, what would be a good value for tau_p so? I was looking in, for exemple, the spider tutorial, and there they use a tau_p value of .5, not so different from my value of .4 (and not .1). Finally: it also mean that if I choose a beta and tau_p pair which yelds a too low value, it won't really affect the equilibrium density of the system, correct? Thanks a lot in advance! Sincerally yours, Jones On 5/3/07, Erik Lindahl [EMAIL PROTECTED] wrote: Hi, On May 3, 2007, at 12:37 PM, Jones de Andrade wrote: Hi Berk! Thanks for your so fast answer! I'll try to look for a different tau_p. I would really feel 4 ps a too high value, even for water systems, but will look around before decision. Anyway, I'm still concerned about the compressibility value. Long time ago in this list I came to this question, and this is how this ended: *** Hi, ** ** Just use the water value for any liquid system (5e-5 or so). * * ** As the manual explains, it only affects the coupling time, not the ** equilibrium pressure. * This is valid for long times, and (as always for pressure) assumes the external coupling to be clearly slower than the internal dynamics. I have no idea how Amber or DLPOLY sets their tau_t with Nose or Parinello-Rahman, but as specified in the Gromacs manual we use the period of average fluctuations at equilibrium. With tau=0.1 the system will very likely never reach that equilibrium. Cheers, Erik ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] using fortran for xtc files
Hi all! About the same subject... Does anybody ever tried to read the topology files from gromacs within fortran? I would accept some C routines for this if necessary... :) Thanks a lot, Jones On 3/24/07, Tsjerk Wassenaar [EMAIL PROTECTED] wrote: Hi Gurpreet, Try to get your hands on the original CONCOORD source code (http://www.mpibpc.gwdg.de/groups/de_groot/concoord/ ; version 1.2 will do). It is written in fortran, and includes the routines to read and write xtc files. Best, Tsjerk On 3/24/07, singh [EMAIL PROTECTED] wrote: Dear Gromacs users, I am trying to read and write xtc files in fortran . Firstly, I couldn't find the file in source directory $(GMXHOME)/src/gmxlib/testxtcf.f in gromacs-3.3.1 as mentioned on http://www.gromacs.org/documentation/reference_3.3/online/xtc.html. Even if i copy the code and compile it using the linker options mentioned on the page, I get the following error In file test.f:12 10 call readxtc(xd,natoms,step,time,box,x,prec,ret) 1 Warning: Label 10 at (1) defined but not used /usr/bin/ld: cannot find -lxtcf collect2: ld returned 1 exit status make: *** [test] Error 1 Any help is appreciated. With Regards, Gurpreet Singh - University of Dortmund Department of Chemistry Physical Chemistry I - Biophysical Chemistry Otto-Hahn Str. 6 D-44227 Dortmund Germany Office: C1-06 room 176 Phone: +49 231 755 3916 Fax: +49 231 755 3901 - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] using fortran for xtc files
Hi David. I would say the .top files. .tpr are not of interest in this point, extra and unnecessary information (at least, I expect). I would prefer this in fortran if possible, cause it would more easy for me to manage. But I don't expect it exists. About the gromacs C files involved: which ones should I look at? Sorry for not making myself clear in the previous message. Thanks a lot in advance, Jones On 3/24/07, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi all! About the same subject... Does anybody ever tried to read the topology files from gromacs within fortran? top or tpr? The latter is out of the question I'd say. I would accept some C routines for this if necessary... :) these are in the code of course, but you basically have to link to the gromacs library. Thanks a lot, Jones On 3/24/07, *Tsjerk Wassenaar* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Hi Gurpreet, Try to get your hands on the original CONCOORD source code (http://www.mpibpc.gwdg.de/groups/de_groot/concoord/ ; version 1.2 will do). It is written in fortran, and includes the routines to read and write xtc files. Best, Tsjerk On 3/24/07, singh [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Dear Gromacs users, I am trying to read and write xtc files in fortran . Firstly, I couldn't find the file in source directory $(GMXHOME)/src/gmxlib/testxtcf.f in gromacs-3.3.1 as mentioned on http://www.gromacs.org/documentation/reference_3.3/online/xtc.html. Even if i copy the code and compile it using the linker options mentioned on the page, I get the following error In file test.f:12 10 call readxtc(xd,natoms,step,time,box,x,prec,ret) 1 Warning: Label 10 at (1) defined but not used /usr/bin/ld: cannot find -lxtcf collect2: ld returned 1 exit status make: *** [test] Error 1 Any help is appreciated. With Regards, Gurpreet Singh - University of Dortmund Department of Chemistry Physical Chemistry I - Biophysical Chemistry Otto-Hahn Str. 6 D-44227 Dortmund Germany Office: C1-06 room 176 Phone: +49 231 755 3916 Fax: +49 231 755 3901 - ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se
[gmx-users] Problems in C8 and C9 chains equilibration
Hi everybody. I would like to ask one question, basically about equilibration of long and flexible alkyl chains. I'm having terrible problems in equilibrating C8 and C9 chains. I've already expanded a lot the box size, but I always fall into segmentation faults. Also tried smaller time steps (my standard is 2fs), doesn't work. Reduction of the rcoulomb, rvdw and similar yields some more steps, but also terrible slower simulations (too much of the electrostatic calculations falling into the reciprocal part). Moreover, in the minimization step, I've tried all the algorithms available for minimization. None of them yields real success. Did anybody successfully equilibrated systems like those, or similar ones like n-octanol? Could anyone please give me some advice on this, any extra trick I forgot or don't know to try to make these molecules run? Thanks a lot in advance for any help! Sincerally yours, Jones ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: FudgeLJ in ffamber - Was: [gmx-users] Re: fudgeQQ (again ...)
Hi Erik. Well, I don't even use the [pairtypes] section in my files. Only use the [pairs] one, in the way explained before. This means, so, that it should not have any problem, and reduce independently the LJ potentials by a factor of 0.5, and coulombic interations by a factor of 0.8333, correct? Thanks a lot for all the help. And hope these files structure examples helps someone else in the future. Thanks a lot. Jones On 2/13/07, Erik Lindahl [EMAIL PROTECTED] wrote: Hi, That should be fine, as long as your [pairtypes] section is empty (i.e., nothing that overrides your generated values). Cheers, Erik ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: FudgeLJ in ffamber - Was: [gmx-users] Re: fudgeQQ (again ...)
Hi David. Ops, you are right. I missexplained, that is what I meant in the question. Well, rewriting it to have the proper and correct question: Well, I don't even use the [pairtypes] section in my files. Only use the [pairs] one, in the way explained before. This means, so, that it should not have any problem, and reduce independently the 1 - 4 LJ potentials by a factor of 0.5, and 1 - 4 coulombic interations by a factor of 0.8333, correct? Tnaks a lot in advance, Sincerally yours, Jones On 2/13/07, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi Erik. Well, I don't even use the [pairtypes] section in my files. Only use the [pairs] one, in the way explained before. This means, so, that it should not have any problem, and reduce independently the LJ potentials by a factor of 0.5, and coulombic interations by a factor of 0.8333, correct? Thanks a lot for all the help. And hope these files structure examples helps someone else in the future. Thanks a lot. Of course this only works for the 1-4 interactions, not the normal LJ and Coulomb interactions. Please see discussion in the manual, chapter 4. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
FudgeLJ in ffamber - Was: [gmx-users] Re: fudgeQQ (again ...)
Hi guys. Well, I'm not exactly trying t reopen an old discussion. I'm trying to see a different aspect from it, as the subject indicates. Since the message reproduced below is the last of the fudges questions, I'm worried about the fact of the fudgeLJ meaning nothing for the simulation. First, is it true, and there is no way around to get a working fudge LJ of 0.5 AND a fudgeQQ of 0.8333 in gromacs simulations? Having this in mind, shouldn't it mean that the ffamber, the amber port to gromacs, have a problem in that point? Specially because it uses, up to the point I could see, the same configurations in the default section? I have deep concerns on this because I would like to move on to gromacs to make the next simulations I'm interested in. My interests in gromacs range from its speed to simplicity and range of analysis programs it already have (and, of course, the cost of the program). But this specific point is a big reason of concern to me, and I would like to see it clarified. Thanks a lot for any help in advance. Sincerally yours, Jones On 12/7/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: I am puzzled about this. In your opinion, when I use genpairs=no, fudgeLJ= 0.5 and fudgeQQ=0.8333, are these scaling factors, 0.5 and 0.8333, useful? On the other hand, when using genpairs=yes, how to set the scaling factor of fudgeLJ and fudgeQQ?$ fudgeQQ is always used no matter what the value of genparis is. (exerpt from http://www.gromacs.org/pipermail/gmx-users/2006-September/023743.html) Each force-field has its own rules (e.g. gen-pairs and FudgeLJ/QQ), but these apply to the information outlined above. For example, gen-pairs does NOT mean generate a [ pairs ] section for the molecule. Instead, it means If LJ-14 epsilon and sigma are not present in a [ pairs ] section entry, and that type of interaction is not explicitly formulated in [ pairtypes ], then it is permissible to use the regular non-bonded parameters, and in that case scale them by FudgeLJ. Therefore your settings indicate that coulombic 1-4 interactions will be scaled by 0.8333 and the pairs must be taken directly from the [ pairs ] or [ pairtypes ] section (and they will NOT be scaled by fudgeLJ). In your case fudgeLJ does not matter (you could change the value and it would not affect your simulation). However, I have always hoped that it is set to 0.5 to indicate that this is what the forcefield developers have done for you and included it in [ pairtypes ] so that it's kind of a reference value for your piece of mind. I was assuming that the previous messages were from an Amber forcefield. Since Amber uses (to my knowledge) [ pairtypes ] instead of genpairs=yes, I was confused by the combination of genpairs=yes and fudgeQQ=0.8333. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: parallel in duals?
Hi David. Well, it wasn't me who did the test. :) My problem is that I cannot try it; I rather have to choose what to buy: extra cores, or extra clock frequency? Does anybody have an advise on this subject? Thank you all... Jones On 8/1/06, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Ok, I know this subject have been discussed in the past. But I started to wander if the basic conclusion (do not use in parallel, you should rather use on job for each core) is still up, and if it is, if there is any hope of change in a foresight future, as well on how much real loss is observed from running one process in parallel when compared to two at the same time. Just try it and you know. Somone reported good performance with hyperhtreading recently (was it you?) I'm wondering about this subject due to the arise of the core 2 duo, as well the expected quad cores from amd and intel and the, semmingly affordable, dual processor motherboards from AMD for both dual and quad-cores. Thanks you all, Jones ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: parallel in duals?
Hi David Fortunatelly, I don't have to buy now... But I have to upgrade only the processor (that's the problem: locked in the sk 939 by now) by the end of the year. Full new computers only next year (seems to be good, anyway), with all new techs (dual procs mb for normal people, 4x cores, etc.). So, since I'm locked in a socket, I'm wandering what's better: the highest clock possible, or less clock with two cores? Thanks a lot... Jones On 8/1/06, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi David. Well, it wasn't me who did the test. :) My problem is that I cannot try it; I rather have to choose what to buy: extra cores, or extra clock frequency? search the mailing list for woodcrest and you will find Florian Haberl's benchmarks. If you have to buy now, Intel woodcrest seems the way to go. Does anybody have an advise on this subject? Thank you all... Jones On 8/1/06, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Ok, I know this subject have been discussed in the past. But I started to wander if the basic conclusion (do not use in parallel, you should rather use on job for each core) is still up, and if it is, if there is any hope of change in a foresight future, as well on how much real loss is observed from running one process in parallel when compared to two at the same time. Just try it and you know. Somone reported good performance with hyperhtreading recently (was it you?) I'm wondering about this subject due to the arise of the core 2 duo, as well the expected quad cores from amd and intel and the, semmingly affordable, dual processor motherboards from AMD for both dual and quad-cores. Thanks you all, Jones ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone:46 18 471 4205fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] parallel in duals?
Ok, I know this subject have been discussed in the past. But I started to wander if the basic conclusion (do not use in parallel, you should rather use on job for each core) is still up, and if it is, if there is any hope of change in a foresight future, as well on how much real loss is observed from running one process in parallel when compared to two at the same time. I'm wondering about this subject due to the arise of the core 2 duo, as well the expected quad cores from amd and intel and the, semmingly affordable, dual processor motherboards from AMD for both dual and quad-cores. Thanks you all, Jones ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Grompp Fudge Problems?
Hi all!.I was trying to simulate a complex cation in MeCN solution and this called my attention: grompp gives me: Generating 1-4 interactions: fudge = 0.5. It's not wrong, since I put this fudge for the VdW interactions, BUT I also placed a different fudge for the intramolecular coulombic interations ( 0.8333), using these lines in the .top file I created:[ defaults ]; nbfunccom-rulegen-pairsfudgeLJfudgeQ12yes 0.5.8333Shouldn't grompp output two fudge parameters instead of only one? How can I be sure that it's using two different fudges, or it simply doesn't output that? Thanks a lot for everything in advance.Jones ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Grompp errors?
Hi all!. I was trying to simulate a complex cation in MeCN solution and I got 2 strange warnings to me: processing topology... WARNING 1 [file ff_emi.itp, line 7]: Overriding atomtype CT WARNING 2 [file ff_emi.itp, line 11]: Overriding atomtype H1 But I did found that strange because, as you can see in the file attached, the entries CT and H1 are just called once. A second thing that called my attention is the following line that grompp gives me: Generating 1-4 interactions: fudge = 0.5. It's not wrong, since I put this fudge for the VdW interactions, BUT I also placed a different fudge for the intramolecular coulombic interations (0.8333), using these lines in the .top file I created: [ defaults ] ; nbfunc com-rulegen-pairs fudgeLJ fudgeQ 12 yes 0.5000 0.8333 Shouldn't grompp output two fudge parameters instead of only one? Are those known issues? I just found those warnings in case of use of standard force fields, what is not the case. The fudge output I could not find any possible answer. Thanks a lot for everything in advance. Jones ; ; emi Force Field Topology File ; [ atomtypes ] ; name mass (a.m.u.) charge (e) ptype sigma (nm) epsilon (kJ/mol) CT12.0112 0.000 A 0.3400 0.4577 NA14.0067 0.000 A 0.3250 0.7113 CR12.0112 0.000 A 0.3400 0.3598 CW12.0112 0.000 A 0.3400 0.3598 H1 1.0080 0.000 A 0.2471 0.0657 HC 1.0080 0.000 A 0.2649 0.0657 H5 1.0080 0.000 A 0.2421 0.0628 H4 1.0080 0.000 A 0.2511 0.0628 [ bondtypes ] ; i j functb0 (nm) kb (kJ/mol.nm^2) CTNA10.1475 141000.81 CTCT10.1526 129704.00 NACR10.1343 199576.80 NACW10.1381 178656.80 CWCW10.1350 229701.61 H1CT10.1090 142256.00 HCCT10.1090 142256.00 H5CR10.1080 153552.80 H4CW10.1080 153552.80 [ angletypes ] ; i j k functth0 (degree) kb (kJ/mol.rad^2) H1CTH1 1109.50146.44 H1CTNA 1109.50209.20 H1CTCT 1109.50209.20 CTCTNA 1109.50209.20 HCCTHC 1109.50146.44 HCCTCT 1109.50209.20 CTNACR 1128.80292.88 CTNACW 1121.20292.88 CRNACW 1120.00292.88 H5CRNA 1120.00146.44 NACRNA 1120.00292.88 H4CWNA 1120.00146.44 H4CWCW 1119.70146.44 NACWCW 1121.20292.88 [ dihedraltypes ] ; j k functphi (degree) cp (kJ/mol.rad^2) mult(n) CTNA 1 0.00 0. 2.0 CTCT 1 0.00 0.6510 3.0 CWCW 1180.0027.8236 2.0 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] intel compiler + amd64: help needed.
Hi all. Of course I want SSE enabled. There is no sense in benching it against different compilers if in one you enable the speed and on the other, and in the other you remove almost every optimization. That's why in the last message I've sent the eror I'm getting in the compilation: * /bin/sh ../../../../libtool --mode=compile /usr/bin/gcc -O3 -ffast-math -funroll-all-loops -fpeel-loops -c -o nb_kernel010_x86_64_sse.lo nb_kernel010_x86_64_sse.s libtool: compile: unable to infer tagged configuration libtool: compile: specify a tag with `--tag' make[5]: ** [nb_kernel010_x86_64_sse.lo] Erro 1 * That's ther error that arises from enabling SSE, and doesn't seems to be related to it (despite it doesn't make too much sense, since it's what is enabled), but only to some kind of libtool option not being corretly passed. From what I could get from the internet, it's related to the swithings in the compiler being used during the compilation process, but I could not get a proper way to get around it for gromacs. And I do think this is last error in the compilations in the way to get a fully working executable gromacs package compiled with the intel compilers on AMD64 machines. The others are just warnings (which didn't look too nice for me anyway, but also can mean nothing), which can be thought about later. Does anybody knows how to go around this specific error? Is it a known issue in gromacs, under some kind of different subject? Thank you all for all the help in advance. :) Jones On 6/2/06, Erik Lindahl [EMAIL PROTECTED] wrote: Hi, Erik: I'm sure about the flags. Not using the ones for SSE3, despite my processor having those. I'll just try to activate those as soon as I get a compiling procedure. By now, I even using the -- disable-x86-64-sse flag for configure, just to be sure. ;) Also, I tried the CC_FOR_BUILD=gcc environment, but despite it has gone throw the invsqrt compilation, I looked in and it was compiling everything with gcc, and nothing with icc. :(You so do NOT want to do disable SSE in Gromacs. To get the extra 2%performance from Intel icc you just killed the assembly loops whichwill reduce your performance by roughly 50%. The Gromacs SSE code is completely portable, and checks if theinstructions are supported at runtime. Yang: Yes, I'm using the intel compiler with emt64. I reinstalled the software step by step specifically to be sure about this point. And I understand that gromacs has an assembly core, and that this is basically the heart of the program speed. But, even thow, 5-10% means something, and every nano-second counts. Specially when you have a big delay to deal with, and that this 10% mean 0.25ns. ;)Even then, after I successfully compile it we will be able to say for sure how much if extra performance (if it yelds any) does the intel compiler gives on AMD64 machines. Moreover, as I said in a long time ago message: I want to use QM/MM with gromacs +cpmd, and at this point I really dislike the idea of compiling one thing with intel (cpmd) and the other with gcc (gromacs). Since I can't make cpmd work on gcc, I'm trying to make gromacs work on intel. ;)We have already tried the intel compiler multiple times (both on ia32and x86-64 platforms), and it gets you roughly 2% extra performance in Gromacs.A really nice thing with icc is that the object format is completelygcc-compatible, so there shouldn't be any problems mixing.Cheers,Erik ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] intel compiler + amd64: help needed.
Ok, I think I got it. Compiled. ;)
About a thousand tricks. I'll publish a tutorial later. But, basically:
1 - Change all invsrt calls to gmx_inv-sqrt (57 entries, 12 files);
2 - Edit the Makefile.in in the
nb_kernels directories, changing the line LTCCASCOMPILE = $(LIBTOOL)
--mode=compile $(CCAS) $(AM_CCASFLAGS) \ by LTCCASCOMPILE =
$(LIBTOOL) --mode=compile --tag=CXX $(CCAS) $(AM_CCASFLAGS) \ in
Makefile.in files;
3 - make disclean (for safety);
4 - Run the configure for gcc, BUT with the following environment and flags(at least):
*
CPPFLAGS=-I/usr/local/lib64/fftw/gnu/include
LDFLAGS=-L/usr/local/lib64/fftw/gnu/lib
CC=/usr/bin/gcc
CXX=/usr/local/intel/bin/icpc
F77=/usr/bin/g77
CFLAGS=-O3 -ffast-math -funroll-all-loops -fpeel-loops
CXXFLAGS=-O3 -axP -xW
F77FLAGS=-O3 -ffast-math -funroll-all-loops -fpeel-loops
*
5 - SAVE the Makefile from nb_kernels directories; special care for the one your compilation will use for sure (machine dependent);
6 - make distcean (for necessity)
7 - Now, run again configure for intel compilers, with the new environment and flags (at least) below:
**
PATH=$PATH /usr/local/intel/bin/ . /usr/local/intel/lib/
LD_LIBRARY_PATH=/usr/local/intel/lib/
CPPFLAGS=-I/usr/local/lib64/fftw/intel/include
LDFLAGS=-L/usr/local/lib64/fftw/intel/lib
CC=/usr/local/intel/bin/icc
CXX=/usr/local/intel/bin/icpc
F77=/usr/local/intel/bin/ifort
CFLAGS=-O3 -axP -xW
CXXFLAGS=-O3 -axP -xW
FFLAGS=-O3 -axP -xW
configure --without-motif-libraries --without-motif-includes --without-x
**
8 - Substitute the new makefiles in nb_kernels directories for the ones you saved in step 5;
9 - Make it.
10 - make install (finally!)
11 - make distclean (to preserve your disk space)
I think I haven't forgot anything. ;)
I can't be sure about this, but I do think that most of the changes
that were necessary to make it run on intel compiler (and, despite I
don't have an intel machine available here, I believe those changes are
necessary for their machines too) can be done with also no harm for the
GCC compilation too. Basically, I'm wasting the CXX environment
variable with the --tag for libtool, but I thik it can be done in
another fashion without touching it. Also, the substitution of
invsqrt for gmx_invsqrt is harmless. Possibly the only difficulty
would be to assure that gcc was used for the mknb compilation with
intel.
But, as I said, it compiled. Now I'm playing a bit with the
--enable-doube and trying to see if it understands mkl for blas and
lapack. Will take about an hour. But, working and running is another
problem at this point. I don't think it would really yeld problems
(will know later), but it still yelds me the following warnings:
###
ghat.c(233): warning #266: function declared implicitly
gh = mk_rgrid(ix,iy,iz);
^
ghat.c(233): warning #967: conversion from int to real={float} ***; sizes do not match
gh = mk_rgrid(ix,iy,iz);
^
fftgrid.c(227): warning #188: enumerated type mixed with another type
gmx_fft_3d_real(grid-fft_setup,dir,grid-ptr,grid-workspace);
^
gmx_fft_fftw3.c(96): warning #1338: arithmetic on pointer to void or function type
pv += 8;
^
gmx_fft_fftw3.c(100): warning #1338: arithmetic on pointer to void or function type
pv += 8;
^
gmx_fft_fftw3.c(186): warning #1338: arithmetic on pointer to void or function type
pv += 8;
^
gmx_fft_fftw3.c(190): warning #1338: arithmetic on pointer to void or function type
pv += 8;
^
gmx_fft_fftw3.c(278): warning #1338: arithmetic on pointer to void or function type
pv += 8;
^
gmx_fft_fftw3.c(282): warning #1338: arithmetic on pointer to void or function type
pv += 8;
^
gmx_fft_fftw3.c(370): warning #1338: arithmetic on pointer to void or function type
pv += 8;
^
gmx_fft_fftw3.c(374): warning #1338: arithmetic on pointer to void or function type
pv += 8;
^
gmx_fft_fftw3.c(463): warning #1338: arithmetic on pointer to void or function type
pv += 8;
^
gmx_fft_fftw3.c(467): warning #1338: arithmetic on pointer to void or function type
pv += 8;
^
gmx_fft_fftw3.c(556): warning #1338: arithmetic on pointer to void or function type
pv += 8;
^
gmx_fft_fftw3.c(560): warning #1338: arithmetic on pointer to void or function type
pv += 8;
^
gmx_dielectric.c(150): warning #266: function declared implicitly
four1(ptr-1,nnx,-1);
^
gmx_nmtraj.c(134): warning #592: variable bDMA is used before its value is set
read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,top,xtop,NULL,box,bDMA);
I'm not sure about
Re: [gmx-users] intel compiler + amd64: help needed.
Hi all!. First, sorry for the delay in getting in touch again. Bureaucracy. :P Second, thanks a lot for everybody for advising on this subject. It's helping me a lot to solve this! :) Anyway, here is where I'm now: Erik: I'm sure about the flags. Not using the ones for SSE3, despite my processor having those. I'll just try to activate those as soon as I get a compiling procedure. By now, I even using the --disable-x86-64-sse flag for configure, just to be sure. ;) Also, I tried the CC_FOR_BUILD=gcc environment, but despite it has gone throw the invsqrt compilation, I looked in and it was compiling everything with gcc, and nothing with icc. :( Yang: Yes, I'm using the intel compiler with emt64. I reinstalled the software step by step specifically to be sure about this point. And I understand that gromacs has an assembly core, and that this is basically the heart of the program speed. But, even thow, 5-10% means something, and every nano-second counts. Specially when you have a big delay to deal with, and that this 10% mean 0.25ns. ;) Even then, after I successfully compile it we will be able to say for sure how much if extra performance (if it yelds any) does the intel compiler gives on AMD64 machines. Moreover, as I said in a long time ago message: I want to use QM/MM with gromacs+cpmd, and at this point I really dislike the idea of compiling one thing with intel (cpmd) and the other with gcc (gromacs). Since I can't make cpmd work on gcc, I'm trying to make gromacs work on intel. ;) David (last but not the least): I removed the -ipo flag from the compilations. Also, I've added --without-motif-libraries --without-motif-includes --without-x flags to the configure script. On the other hand, I've been greping a bit the directories for the invsqrt calls My God, it's not the heart of the program, it's the sinapses among its neurones. Am I wrong, or there is about some thousands of those calls to be changed? Is it right? If it is, just let me know, cause I'm tracking those down (finding a script way to back up original files before edition.) and at the same time trying to find some sort of magical flag to convince icc to *not* use the invsqrt function or the math.h file at all (second choice seems to me a bit too strong). Seems that if it can be done on a flag it will be really helpfull (and easier) for most of the users. The good new is that there is no other error message in the ompilation, as I can see (And just a few warnings to see later, since they look more or less pointless). By the way, can I ask you what was the mknb program for, anyway? :) Again, thanks a lot to everybody in advance, for all the help an advices provided up to now! If I manage to finish this one, I promisse to post those extra benchmarks too, as well as a tutorial on how to compile gromacs on AMD64 machines with non-sense copilers. ;) JonesOn 6/1/06, David van der Spoel [EMAIL PROTECTED] wrote: make[3]: ** [grompp] Erro 1 make[3]: Leaving directory `/home/johannes/src/gromacs/gromacs-3.3/src/kernel' make[2]: ** [all-recursive] Erro 1 make[2]: Leaving directory `/home/johannes/src/gromacs/gromacs- 3.3/src' make[1]: ** [all] Erro 2 make[1]: Leaving directory `/home/johannes/src/gromacs/gromacs-3.3/src' make: ** [all-recursive] Erro 1 ** Trying withou the -ipo flag now. It still yelds the same weird warning (warning #147: declaration is incompatible with double invsqrt(double) (declared at line 565 of /usr/local/intel/include/math.h) rename all gromacs invsqrt calls to gmx_invsqrtbe assured that invsqrt didn't exist in the intel compiler in previousreleases, but now that it does we'll have to adapt it seems.ipo is useless for gromacs. do also turn off X11 at the configure stage--David.David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Swedenphone:46 18 471 4205fax: 46 18 511 755[EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] intel compiler + amd64: help needed.
Hi all. On 6/1/06, David van der Spoel [EMAIL PROTECTED] wrote: Trying withou the -ipo flag now. It still yelds the same weird warning (warning #147: declaration is incompatible with double invsqrt(double) (declared at line 565 of /usr/local/intel/include/math.h)rename all gromacs invsqrt calls to gmx_invsqrt Just a stupid question. No, unfortunatelly I still didn't found a magic flag (trying to be in touch with the intel premier support still). Anyway, I was trying to grep every invsqrt in gromacs directories, and after verbosing out strings like invsqrta, _invsqrt, invsqrtdata, vecinvsqrt, invsqrtm, invsqrtfracttab and invsqrtexptab, and also some comments stuff... Well, the command line below: grep -Hni 'invsqrt' -r * | grep -v 'Arquivo' | grep -v '#' | grep -v 'icc' | grep -v 'gcc' | grep -v 'pgi' | grep -v 'intel' | grep -vi '.bak' | grep -v 'html' | grep -vi 'invsqrta' | grep -v '_invsqrt' | grep -v 'invsqrtdata' | grep -v 'vecinvsqrt' | grep -v 'invsqrtm' | grep -v 'Software' | grep -v 'fast' | grep -v 'invsqrtfracttab' | grep -v 'invsqrtexptab' | grep -v 'version' I finally arrived to 57 entries to invsqrt. Just before start, and since I'm not good at C (F90 addicted), are those 57 entries in only 12 files all that I should have to modify (I expected little more)? Just in case, I'm attaching the output from that load of piped greps. I'll be working on it tonight, and hope tomorrow I'll have more news on it. I'll, if those are the only lines of code to change. Despite of that, I've made a trial without the --disable-x86-64-sse flag for config. The compilation fails at another point now: * /bin/sh ../../../../libtool --mode=compile /usr/bin/gcc -O3 -ffast-math -funroll-all-loops -fpeel-loops -c -o nb_kernel010_x86_64_sse.lo nb_kernel010_x86_64_sse.s libtool: compile: unable to infer tagged configuration libtool: compile: specify a tag with `--tag' make[5]: ** [nb_kernel010_x86_64_sse.lo] Erro 1 * I found some information on this kind of error from libtool on google (something about compiler changing in different parts of compilation process), but I'm not finding a way around this. Does anybody has any idea on this, please? Thanks a lot for everything in advance. Jones include/vec.h:54: real invsqrt(real x) include/vec.h:146:static inline real invsqrt(real x) include/vec.h:466: cos=ip*invsqrt(ipa*ipb);/* 7 */ include/vec.h:674: linv=invsqrt(norm2(src)); src/mdlib/csettle.c:256:axlng = invsqrt(xaksxd * xaksxd + yaksxd * yaksxd + zaksxd * zaksxd); src/mdlib/csettle.c:257:aylng = invsqrt(xaksyd * xaksyd + yaksyd * yaksyd + zaksyd * zaksyd); src/mdlib/csettle.c:258:azlng = invsqrt(xakszd * xakszd + yakszd * yakszd + zakszd * zakszd); src/mdlib/csettle.c:296: cosphi = tmp*invsqrt(tmp); src/mdlib/csettle.c:305: cospsi = tmp2*invsqrt(tmp2); src/mdlib/csettle.c:323: sinthe = (alpa * gama - beta * tmp2*invsqrt(tmp2)) / al2be2; src/mdlib/csettle.c:328: costhe = tmp2*invsqrt(tmp2); src/mdlib/vsite.c:307: c=b*invsqrt(iprod(temp,temp)); src/mdlib/vsite.c:328: invdij = invsqrt(iprod(xij,xij)); src/mdlib/vsite.c:334: b1 = b*invsqrt(iprod(xp,xp)); src/mdlib/vsite.c:380: d=c*invsqrt(iprod(temp,temp)); src/mdlib/vsite.c:631: invl=invsqrt(iprod(xix,xix)); src/mdlib/vsite.c:703: invdij = invsqrt(iprod(xij,xij)); src/mdlib/vsite.c:710: invdp = invsqrt(iprod(xperp,xperp)); src/mdlib/vsite.c:860: invl=invsqrt(iprod(xix,xix)); src/mdlib/clincs.c:199: rlen = invsqrt(tmp0*tmp0+tmp1*tmp1+tmp2*tmp2); src/mdlib/clincs.c:287: mvb = blc[b]*(len - u0*invsqrt(u0)); src/mdlib/clincs.c:364:li-blc[i] = invsqrt(invmass[a1] + invmass[a2]); src/mdlib/clincs.c:586:len = r2*invsqrt(r2); src/tools/gmx_nmeig.c:90: mass_fac=invsqrt(top-atoms.atom[i].m*top-atoms.atom[k].m); src/tools/gmx_nmeig.c:112:mass_fac = invsqrt(top-atoms.atom[j].m); src/tools/gmx_nmeig.c:156: mass_fac=invsqrt(top-atoms.atom[iatom].m*top-atoms.atom[katom].m); src/tools/gmx_nmeig.c:174:mass_fac = invsqrt(top-atoms.atom[j].m); src/tools/calcpot.c:123: rinv1O= invsqrt(rsqO); src/gmxlib/orires.c:302:invr = invsqrt(r2); src/gmxlib/orires.c:460: invr = invsqrt(r2); src/gmxlib/disre.c:160: rt_1 = invsqrt(rt2); src/gmxlib/disre.c:328: weight_rt_1 = invsqrt(rt2); src/gmxlib/ewald_util.c:200: rinv = invsqrt(dr2); src/gmxlib/ewald_util.c:287: rinv = invsqrt(dr2); src/gmxlib/nonbonded/nb_free_energy.c:159:rinv = invsqrt(rsq); src/gmxlib/shift_util.c:237: R_1 = invsqrt(r2); src/gmxlib/shift_util.c:239: R = invsqrt(R_2);
Re: [gmx-users] intel compiler + amd64: help needed.
Hi all. :)
Last message today. It seems that I succeded in switching all invsqrt
functins to a new gmx_invsqrt. Just 57 in the 12 files below:
***
include/vec.h
src/mdlib/csettle.c
src/mdlib/vsite.c
src/mdlib/clincs.c
src/tools/gmx_nmeig.c
src/tools/calcpot.c
src/gmxlib/orires.c
src/gmxlib/disre.c
src/gmxlib/ewald_util.c
src/gmxlib/nonbonded/nb_free_energy.c
src/gmxlib/shift_util.c
src/gmxlib/bondfree.c
*
With this, and with the configure flag --disable-x86-64-sse, The
compilation yelded only warnings. I reproduce they below. Should I be
worried about any of them? The ones involving FFTs, and the ones about
variables being used before declaration do not look too nice to me:
ghat.c(233): warning #266: function declared implicitly
ghat.c(233): warning #967: conversion from int to real={float} ***; sizes do not match
fftgrid.c(227): warning #188: enumerated type mixed with another type
gmx_fft_fftw3.c(96): warning #1338: arithmetic on pointer to void or function type
gmx_fft_fftw3.c(100): warning #1338: arithmetic on pointer to void or function type
gmx_fft_fftw3.c(186): warning #1338: arithmetic on pointer to void or function type
gmx_fft_fftw3.c(190): warning #1338: arithmetic on pointer to void or function type
gmx_fft_fftw3.c(278): warning #1338: arithmetic on pointer to void or function type
gmx_fft_fftw3.c(282): warning #1338: arithmetic on pointer to void or function type
gmx_fft_fftw3.c(370): warning #1338: arithmetic on pointer to void or function type
gmx_fft_fftw3.c(374): warning #1338: arithmetic on pointer to void or function type
gmx_fft_fftw3.c(463): warning #1338: arithmetic on pointer to void or function type
gmx_fft_fftw3.c(467): warning #1338: arithmetic on pointer to void or function type
gmx_fft_fftw3.c(556): warning #1338: arithmetic on pointer to void or function type
gmx_fft_fftw3.c(560): warning #1338: arithmetic on pointer to void or function type
gmx_dielectric.c(150): warning #266: function declared implicitly
gmx_nmtraj.c(134): warning #592: variable bDMA is used before its value is set
Unfortunatelly, as said in the last message, the code still complains
when I try to compile it without the --disable-x86-64-sse flag in the
configure script. Reallt strange is that I don't see why it complains
in one case and not in the other, but the configure fails when tries
to use libtool:
*
/bin/sh ../../../../libtool --mode=compile /usr/bin/gcc -O3
-ffast-math -funroll-all-loops -fpeel-loops -c -o
nb_kernel010_x86_64_sse.lo nb_kernel010_x86_64_sse.s
libtool: compile: unable to infer tagged configuration
libtool: compile: specify a tag with `--tag'
make[5]: ** [nb_kernel010_x86_64_sse.lo] Erro 1
*
Googling this error, I found it related to the changes in the compiler,
but I could not get a way to fix it for gromacs. Did anyone crossed
with this error before, in other context maybe? Any idea on how to fix
it?
Anyway, thanks a lot to everybody for all in advance. If it was not
your help, it would not be possible to get this far already! :) Almost
there now, it seems! :)
Thank you all in advance again.
Jones
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Re: [gmx-users] intel compiler + amd64: help needed.
Hi David. First, thanks for your time. ;) Unfortunatelly, it seems that the simple flag it is not quite enough still... :( If it was not a well known fact that intel compiler yelds you some extra performance for gromacs, and if I would not want to try to make QM/MM of gromacs+cpmd (and, in this case, I DO prefer to not mix compilers), I would have gave up this compiler already. :( Well, here is what I got: I tried to put the suggested CFLAGS as an option in the make line, and that didn't work. So I set the CFLAGS by hand before the make. Since tht was not enough too, I did the compilations by hand, one compilation line after the other. Here we go (before anybody asks: it failed at the exact same point... :( ): * CruNumMac# rm *.o CruNumMac# rm mknb CruNumMac# /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I. -I../../../../src -g -c -o mknb.o mknb.c CruNumMac# /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I. -I../../../../src -g -c -o mknb_metacode.o mknb_metacode.c CruNumMac# /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I. -I../../../../src -g -c -o mknb_common.o mknb_common.c CruNumMac# /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I. -I../../../../src -g -c -o mknb_declarations.o mknb_declarations.c CruNumMac# /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I. -I../../../../src -g -c -o mknb_outerloop.o mknb_outerloop.c CruNumMac# /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I. -I../../../../src -g -c -o mknb_innerloop.o mknb_innerloop.c mknb_innerloop.c(362): warning #188: enumerated type mixed with another type mknb_func.coul=coulsave; ^ mknb_innerloop.c(363): warning #188: enumerated type mixed with another type mknb_func.vdw=vdwsave; ^ CruNumMac# /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I. -I../../../../src -g -c -o mknb_interactions.o mknb_interactions.c CruNumMac# /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I. -I../../../../src -g -o mknb mknb.o mknb_metacode.o mknb_common.o mknb_declarations.o mknb_outerloop.o mknb_innerloop.o mknb_interactions.o CruNumMac# rm -f kernel-stamp CruNumMac# ./mknb -software_invsqrt Gromacs nonbonded kernel generator (-h for help) Generating single precision functions in C. Using Gromacs software version of 1/sqrt(x). Falha de segmentação Unfortunately, it means that I'm back to the beggining. I've also tried the -debug extended option instead of -g, and that yelded exactly same results... :( Any suggestion at this point? Thanks a lot in advance. JonesOn 5/31/06, David van der Spoel [EMAIL PROTECTED] wrote: The error I get is still the following: ** ./mknb -software_invsqrt Gromacs nonbonded kernel generator (-h for help) Generating single precision functions in C. Using Gromacs software version of 1/sqrt(x). make[5]: *** [kernel-stamp] Falha de segmentação make[5]: Leaving directory `/home/johannes/src/gromacs/gromacs-3.3/src/gmxlib/nonbonded/nb_kernel' make[4]: ** [all-recursive] Erro 1 *your problem here is that the mknb program crashes with a SEGV, which is weird. You could trymake CFLAGS=-g mknb./mknb -software_invsqrtmake installObviously if mknb crashed due to compiler bugs then you might not wantto use that compiler anyway, but if there is a real problem in the program you will be able to debug it.--David.David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Swedenphone:46 18 471 4205fax: 46 18 511 755[EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] intel compiler + amd64: help needed.
Hi David. Thanks a lot. But almost there. first, coulsave is already n int type variable: int vdwsave,coulsave,read_from_mem,write_to_mem; (line 294) So, the change from: mknb_func.coul=coulsave; mknb_func.vdw=vdwsave; To: mknb_func.coul=(int)coulsave; mknb_func.vdw=(int)vdwsave; Was pointless, and unfortunatelly yelded the same crash. Unfortunatelly, fortran addicted (seems that its more than time to try a few other things, tastes and sensations out...), so I don't know how to write the new declaration line. Just in advance: if I search in the file for the coulsave, I found those two lines AND the following: coulsave=mknb_func.coul; vdwsave=mknb_func.vdw; Am I wrong, or does it means that coulsave is used as both (if yes, how hell someone could compile it in first place? :P and even get extra performance!) as we fear? Thanks a lot in advance for everything. Jones On 5/31/06, David Mathog [EMAIL PROTECTED] wrote: mknb_innerloop.c(362): warning #188: enumerated type mixed withanother type mknb_func.coul=coulsave; ^I don't have the most recent source code on my machine,but the way around this may be to use an explicit cast.Assuming that coulsave is the enumerated type and mknob_func.coulis an int then: mknb_func.coul = (int) coulsave; will probably shut the compiler up.If mknb_func.coul isenumerated and coulsave is an int you will probably haveto change the type of coulsave to the same enumerated typewherever it is declared.Hopefully the code doesn't use coulsave as both an int and an enumerated type, if it does the compilerwill probably let you know :-).Regards,David Mathog[EMAIL PROTECTED]Manager, Sequence Analysis Facility, Biology Division, Caltech ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] intel compiler + amd64: help needed.
Hi David. And how could I do it? I mean, isn't mknb a significative piece of the code? What is it for? Would not that it yeld any problem? And how to do it? Am I wrong, or should I first I run configure as it is for gcc, save the mknb msakefile on it's directory, then configure for icc, substitute it by the old Mkefile in the mknb directory and then make? (Trying this now) Thanks in advance for everything. JonesOn 5/31/06, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi all. Program received signal SIGSEGV, Segmentation fault. 0x2b15a88c in __find_specmb () from /lib64/tls/libc.so.6 (gdb) where #00x2b15a88c in __find_specmb () from /lib64/tls/libc.so.6 #10x2b140e6f in vfprintf () from /lib64/tls/libc.so.6 #20x2b15e2a9 in vsprintf () from /lib64/tls/libc.so.6 #30x2b149568 in sprintf () from /lib64/tls/libc.so.6 #40x0040248b in mknb_code (format=0x40cd2e s) at mknb_metacode.c:282 #50x00401aaf in mknb_declare_real (name=0x7fffd0d0 ix1,iy1,iz1,fix1,fiy1,fiz1) at mknb_metacode.c:104 #60x00403e62 in mknb_declare_variables () at mknb_declarations.c:258 #70x00400fef in mknb_write_function () at mknb.c:154 #80x004017cf in main (argc=1, argv=0x7fffd628) at mknb.c:348 Well, what does this kind of stuff means? It worries about the libc 4 times, but also about the other files. :( What shall I look at?It shows where in the GROMACS code the error started (mknb_metacode.c282) and that the Intel compiler f*cked up the va_args. I suggest you compile the mknb program with gcc and the rest with icc. David Mathog: thanks also. But, how could I fix that? Thanks a lot for everything. Jones On 5/31/06, *David van der Spoel* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: gdb where it will tell you the line in the mknb this was called from. if you call a library function with garbage data it may crash there... -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:46 18 471 4205fax: 46 18 511 755 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED][EMAIL PROTECTED] mailto:[EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php --David.David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Swedenphone:46 18 471 4205fax: 46 18 511 755[EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] intel compiler + amd64: help needed.
Hi all. First of all, thanks everybody for the help. ;) Yang, I know, I know. I should keep to the GNU. But lets say that I get addicted to the intel compiler on a cpmd winter school, when it appeared in front of me as the only freely available for both amd and intel cpus fortran90 compiler. Since it also came with performance for free, that was a good deal. I also have just a handfull of tuning flags I use for icc and ifort. But, like everybody in here, we choose the machines for performance (which means, first corret result, and later speed), same goes for me for the compilers. Moreover, as I said before: I wana try QM/MM, and CPMD doesn't work with gcc. Back to the subject: David, thanks for the piece of gmx4 code. Unfortunatelly, it don't work. I deleted all the objects from the directory before trying to compile to assure that, and it yelded the same error. On the other hand, the trick of compiling just mknb in gcc, and the rest with icc got a bit farther, before crashing... but still gone with about a thousand of weird warnings. I'm sending the window desktop outputs attached in this message. Anyway, in order to make that trick, I've used the following script: export CPPFLAGS=-I/usr/local/lib64/fftw/gnu/include export LDFLAGS=-L/usr/local/lib64/fftw/gnu/lib export CC=/usr/local/bin/gcc export CFLAGS=-O3 -ffast-math -funroll-all-loops -fpeel-loops make distclean ./configure --prefix=/usr/local/bin/chemistry/gromacs/ISI/ --with-fft=fftw3 cp ./src/gmxlib/nonbonded/nb_kernel/Makefile ./Makefile.mknb.gcc cp ./src/gmxlib/nonbonded/nb_kernel_ia32_3dnow/Makefile ./Makefile.mknb_kernel_ia32_3dnow.gcc cp ./src/gmxlib/nonbonded/nb_kernel_ia32_sse/Makefile ./Makefile.mknb_kernel_ia32_sse.gcc cp ./src/gmxlib/nonbonded/nb_kernel_ia32_sse2/Makefile ./Makefile.mknb_kernel_ia32_sse2.gcc cp ./src/gmxlib/nonbonded/nb_kernel_x86_64_sse/Makefile ./Makefile.mknb_kernel_x86_64_sse.gcc cp ./src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/Makefile ./Makefile.mknb_kernel_x86_64_sse2.gcc export PATH=$PATH /usr/local/intel/bin/ . /usr/local/intel/lib/ export LD_LIBRARY_PATH=/usr/local/intel/lib/ export CPPFLAGS=-I/usr/local/lib64/fftw/intel/include export LDFLAGS=-L/usr/local/lib64/fftw/intel/lib export CC=/usr/local/intel/bin/icc export CXX=/usr/local/intel/bin/icpc export F77=/usr/local/intel/bin/ifort export CFLAGS= export CXXFLAGS= export FFLAGS= export CFLAGS=-O3 -axP -xW -ipo -static export CXXFLAGS=-O3 -axP -xW -ipo -static export FFLAGS=-O3 -axP -xW -ipo -static make distclean ./configure --prefix=/usr/local/bin/chemistry/gromacs/ISI/ --with-fft=fftw3 --disable-x86-64-sse cp ./src/gmxlib/nonbonded/nb_kernel/Makefile ./Makefile.mknb.icc cp ./src/gmxlib/nonbonded/nb_kernel_ia32_3dnow/Makefile ./Makefile.mknb_kernel_ia32_3dnow.icc cp ./src/gmxlib/nonbonded/nb_kernel_ia32_sse/Makefile ./Makefile.mknb_kernel_ia32_sse.icc cp ./src/gmxlib/nonbonded/nb_kernel_ia32_sse2/Makefile ./Makefile.mknb_kernel_ia32_sse2.icc cp ./src/gmxlib/nonbonded/nb_kernel_x86_64_sse/Makefile ./Makefile.mknb_kernel_x86_64_sse.icc cp ./src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/Makefile ./Makefile.mknb_kernel_x86_64_sse2.icc cp ./Makefile.mknb.gcc ./src/gmxlib/nonbonded/nb_kernel/Makefile cp ./Makefile.mknb_kernel_ia32_3dnow.gcc ./src/gmxlib/nonbonded/nb_kernel_ia32_3dnow/Makefile cp ./Makefile.mknb_kernel_ia32_sse.gcc ./src/gmxlib/nonbonded/nb_kernel_ia32_sse/Makefile cp ./Makefile.mknb_kernel_ia32_sse2.gcc ./src/gmxlib/nonbonded/nb_kernel_ia32_sse2/Makefile cp ./Makefile.mknb_kernel_x86_64_sse.gcc ./src/gmxlib/nonbonded/nb_kernel_x86_64_sse/Makefile cp ./Makefile.mknb_kernel_x86_64_sse2.gcc ./src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/Makefile make The output from it isn't attached. :( Sorry, The gziped file is too big for the list limits. Anyway, despite lots of warnings, the compilations ends dieing in here: * /tmp/ipo_iccpmJSXr.c: undefined reference to `interaction_function' /tmp/ipo_iccpmJSXr.o(.text+0x2edde):/tmp/ipo_iccpmJSXr.c: undefined reference to `interaction_function' /tmp/ipo_iccpmJSXr.o(.text+0x2ede6):/tmp/ipo_iccpmJSXr.c: undefined reference to `interaction_function' /tmp/ipo_iccpmJSXr.o(.text+0x2f1ca):/tmp/ipo_iccpmJSXr.c: undefined reference to `_gmx_error' /tmp/ipo_iccpmJSXr.o(.text+0x2f29b): In function `DS_Init': /tmp/ipo_iccpmJSXr.c: undefined reference to `save_calloc' /tmp/ipo_iccpmJSXr.o(.text+0x2f64d):/tmp/ipo_iccpmJSXr.c: undefined reference to `debug' /tmp/ipo_iccpmJSXr.o(.text+0x2f682):/tmp/ipo_iccpmJSXr.c: undefined reference to `debug' /tmp/ipo_iccpmJSXr.o(.text+0x2f6f6):/tmp/ipo_iccpmJSXr.c: undefined reference to `debug' /tmp/ipo_iccpmJSXr.o(.text+0x2f76c): In function `init_block2': /tmp/ipo_iccpmJSXr.c: undefined
[gmx-users] Re: Benching against different compilers - Help needed
Hi again. Well, here we go: On 4/30/06, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Up to now, I could finally compile it with Portland, in both single and double precision version. But, on the other hand, while the single precision works properly, the double precision fails in some tests, like the mixed test on the tutor directory. It yelds me the following error message: this is hard to debug, but what you could do is run the same tpr with different executables and do gmxcheck -e -e2 to compare energies. that might give a clue. step 0 Step 1 Warning: pressure scaling more than 1%, mu: 1.01018 1.02193 1.08117 Step 2 Warning: pressure scaling more than 1%, mu: 1.01124 1.00787 1.08362 Step 143 Warning: pressure scaling more than 1%, mu: 1.00304 1.00017 1.01009 step 240, remaining runtime:40 s Program mdrun_d, VERSION 3.3 Source code file: stat.c, line: 283 Fatal error: XTC error Ok, I did gmxcheck for both double precision versions of gromacs I got: one compiled with GCC, and the other with PGI. Here is what I got. Everything looks to be ugly and different, btw; no idea where to look first: * comparing energy file ener.edr and ener2.edr Opened ener.edr as double precision energy file Opened ener2.edr as double precision energy file There are 44 terms in the energy files There are 44 terms to compare in the energy files Reading frame 1 time0.000 Pressure (bar) step 0: 2.26575e+06, step 0: -1212.92 pV step 0: 3.53269e+06, step 0: -1891.14 Vir-XX step 0: -475104, step 0: 2135.61 Vir-XY step 0:491116, step 0: -544.385 Vir-XZ step 0:763516, step 0: 180.112 Vir-YX step 0:491225, step 0: -544.385 Vir-YY step 0: -1.02488e+06, step 0: 2008.1 Vir-YZ step 0: -1.53177e+06, step 0: 558.876 Vir-ZX step 0:763218, step 0: 180.112 Vir-ZY step 0: -1.53059e+06, step 0: 558.876 Vir-ZZ step 0: -3.79554e+06, step 0: 2209.48 Pres-XX (bar)step 0:610883, step 0: -1286.57 Pres-XY (bar)step 0: -630004, step 0: 664.233 Pres-XZ (bar)step 0: -979427, step 0: -271.252 Pres-YX (bar)step 0: -630144, step 0: 664.233 Pres-YY (bar)step 0:1.3161e+06, step 0: -1124.86 Pres-YZ (bar)step 0: 1.96481e+06, step 0: -753.997 Pres-ZX (bar)step 0: -979044, step 0: -271.252 Pres-ZY (bar)step 0:1.9633e+06, step 0: -753.997 Pres-ZZ (bar)step 0: 4.87027e+06, step 0: -1227.32 #Surf*SurfTenstep 0: 9.18092e+06, step 0: -50.7689 Reading frame 3 time0.100 Anglestep 50: 1570.43, step 50: 306.588 LJ (SR) step 50: -449.51, step 50: -188.033 Disper. corr.step 50: -48.4547, step 50: -193.09 Coulomb (SR) step 50: -1821.5, step 50: -14751.3 Potentialstep 50: -749.035, step 50: -14825.8 Kinetic En. step 50: 4695.12, step 50: 3702.53 Total Energy step 50: 3946.09, step 50: -11123.3 Temperature step 50: 402.631, step 50: 317.511 Pressure (bar) step 50: 35297.3, step 50: -836.341 Box-Xstep 50: 6.85856, step 50: 4.68882 Box-Ystep 50: 3.81751, step 50: 2.34589 Box-Zstep 50: 3.93067, step 50: 2.34792 Volume step 50: 102.915, step 50: 25.8259 Density (SI) step 50: 174.458, step 50: 695.211 pV step 50:218762, step 50: -1300.74 Vir-XX step 50: -34277.1, step 50: 1588.65 Vir-XY step 50: -19728.5, step 50: 108.132 Vir-XZ step 50: -14866.4, step 50: 14.285 Vir-YX step 50: -20282.2, step 50: 108.132 Vir-YY step 50: -185709, step 50: 2157.54 Vir-YZ step 50: -102950, step 50: -196.053 Vir-ZX step 50: -15598.4, step 50: 14.285 Vir-ZY step 50: -102762, step 50: -196.053 Vir-ZZ step 50: -103462, step 50: 1907.44 Pres-XX (bar)step 50: 11541.9, step 50: -445.503 Pres-XY (bar)step 50: 6367.62, step 50: -183.086 Pres-XZ (bar)step 50: 4787.13, step 50: -18.5143 Pres-YX (bar)step 50:6546.3, step 50: -183.086 Pres-YY (bar)step 50: 60435.8, step 50: -1150.69 Pres-YZ (bar)step 50: 33194.4, step 50: 289.951 Pres-ZX (bar)step 50
[gmx-users] Compressibility in NpT: What value to input?
Hi all. Ok, this may sound like a stupid question, since the equations of the barostats clearly states the compressibility constant in it. But, in other programas I used to do NpT (usually with Nosè-Hoover) simulations, like DL_Poly and MDynaMix, I never had to input this parameter. Only reference pressure and pressure coupling time were needed. Does anybody here have a clue on it? Or, in a better way to ask: how can I make an NpT simulation, of a liquid with an unknown compressibility and which I maybe would like to estimate throw simulation, preferably without running in the error of inputing this as parameter? Thanks in advance. Jones ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Compressibility in NpT: What value to input?
Hi! I've seen it on the manual too. But one doubt arise: Wouldn't that value affect some other pressure dependent properties when calculated, like exactly the liquid compressibility Thanks a lot in advance! Jones On 5/3/06, Erik Lindahl [EMAIL PROTECTED] wrote: Hi,Just use the water value for any liquid system (5e-5 or so).As the manual explains, it only affects the coupling time, not theequilibrium pressure.Cheers,ErikOn May 3, 2006, at 8:54 PM, Jones de Andrade wrote: Hi all. Ok, this may sound like a stupid question, since the equations of the barostats clearly states the compressibility constant in it. But, in other programas I used to do NpT (usually with Nosè-Hoover) simulations, like DL_Poly and MDynaMix, I never had to input this parameter. Only reference pressure and pressure coupling time were needed. Does anybody here have a clue on it? Or, in a better way to ask: how can I make an NpT simulation, of a liquid with an unknown compressibility and which I maybe would like to estimate throw simulation, preferably without running in the error of inputing this as parameter? Thanks in advance. Jones ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php___ gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Mix solvent
Hi! Ops! I forgot to paste the web address! :P Here it goes: http://www.ime.unicamp.br/~martinez/packmol/ And, yes: It's GPL too. ;) JonesOn 4/27/06, Mark Abraham [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi. Well, I don't know if the list allows the indication of out-gromacs programs. Anyway, you can download the packmol program (). Simple and easy for this kind of stuff (I use it a lot).Non-gromacs solutions are fine - we're interested in solutions toproblems and when there's no money involved (here) the idea is to getthe job done simply! Mark___gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] .Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Benching against different compilers - Help needed
Hi all. Well, some time ago I decided to bench gromacs on AMD64 machines compiled with different compilers (both single and double precision, both internal and external blas and lapack, just FFTw 3 for fourier) in order to see which one performs better. To time, I have available GCC, PGI and Intel compilers. Pathscale is a future option. Unfortunatelly, I was able to properly compile it just with GCC (all 4 flavours, despite the fact that the external libraries of ACML didn't seem to improve so much the performance as I expected), but failed on both PGI and Intel compilers at different points. So, I'm asking for help on those compilation issues. For Intel, the compilation ends up with a segmentation fault at the following point: *** ./mknb -software_invsqrt Gromacs nonbonded kernel generator (-h for help) Generating single precision functions in C. Using Gromacs software version of 1/sqrt(x). make[5]: *** [kernel-stamp] Falha de segmentação make[5]: Leaving directory `/home/johannes/src/gromacs/gromacs-3.3/src/gmxlib/nonbonded/nb_kernel' make[4]: ** [all-recursive] Erro 1 *** And, for PGI, it dies at the following point (after using the --without-x --without-motif-libraries -- without-motif-includes flags for configure): source='gmx_sgangle.c' object='gmx_sgangle.lo' libtool=yes \ DEPDIR=.deps depmode=none /bin/sh ../../config/depcomp \ /bin/sh ../../libtool --mode=compile --tag=CC /usr/local/pgi/linux86-64/6.0/bin/pgcc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\/usr/local/bin/chemistry/gromacs/PSI//share/top\ -I/usr/local/lib64/fftw/pgi/include -tp=k8-64 -fastsse -Mipa=fast -Mipa=inline -c -o gmx_sgangle.lo gmx_sgangle.c /usr/local/pgi/linux86-64/6.0/bin/pgcc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\/usr/local/bin/chemistry/gromacs/PSI//share/top\ -I/usr/local/lib64/fftw/pgi/include -tp=k8-64 -fastsse -Mipa=fast -Mipa=inline -c gmx_sgangle.c -o gmx_sgangle.o PGC-S-0090-Scalar data type required for logical expression (gmx_sgangle.c: 313) PGC-S-0090-Scalar data type required for logical expression (gmx_sgangle.c: 320) PGC/x86-64 Linux/x86-64 6.0-5: compilation completed with severe errors ** Did anyone run into those problems before when trying to compile gromacs with those compilers? Any help will be very welcome. :) Thanks a lot in advance, Jones P.S.: I'm using the mixed run simulation of the tutor directory as a compilation test. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Installation Error on an Athlon64 with Intel Compiler
Hi again! Well, still having problems: /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I. -I../../../../src -c -o mknb_interactions.o mknb_interactions.c /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I. -I../../../../src -o mknb mknb.o mknb_metacode.o mknb_common.o mknb_declarations.o mknb_outerloop.o mknb_innerloop.o mknb_interactions.o rm -f kernel-stamp ./mknb -software_invsqrtWould like to go to/home/johannes/src/gromacs/gromacs-3.3/src/gmxlib/nonbonded/nb_kerneland run this command../mknb -software_invsqrt Here we go. Following the instructions, we get: [EMAIL PROTECTED]:~/src/gromacs/gromacs-3.3/src/gmxlib/nonbonded/nb_kernel su root Password: linux:/home/johannes/src/gromacs/gromacs-3.3/src/gmxlib/nonbonded/nb_kernel # export LD_LIBRARY_PATH=/usr/local/intel/lib/ linux:/home/johannes/src/gromacs/gromacs-3.3/src/gmxlib/nonbonded/nb_kernel # ./mknb -software_invsqrt Gromacs nonbonded kernel generator (-h for help) Generating single precision functions in C. Using Gromacs software version of 1/sqrt(x). Falha de segmentação So, back to the beggining. Still getting an segmentation fault at this point. I really don't think it's due to a 32/64bits issue, cause everything in here, specially compilers and libraries, is being installed only the 64 bits version. Anyway, how could I verify this possibility again, and find out if it's this the problem or not? Any other idea of what could be causing this error in here (yes, I hate the segmentation faults too)? Thanks a lot for everything to all. Jones ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] FFTW installation error: cannot compile asimpleFortran program
Hi all! Ok, I did not acquired to compile gromacs with intel yet, but now I'm also facing problems with PGI compilers (which also has the extra problem of needin to be redownloaded soon). Just in case someone asks: I'm trying to benchmark gromacs in A64s with different compilers. ;) Well, PGI is dieing here: . . . /usr/local/pgi/linux86-64/6.0/bin/pgcc -tp=k8-64 -fastsse -Mipa=fast -Mipa=inline -o grompp topio.o toppush.o topcat.o topshake.o convparm.o tomorse.o sorting.o splitter.o vsite_parm.o readir.o add_par.o topexcl.o toputil.o topdirs.o grompp.o -L/usr/local/lib64/fftw/pgi/lib ../mdlib/.libs/libmd.a -L/usr/X11R6/lib64 -L/usr/X11/lib ../gmxlib/.libs/libgmx.a -lnsl /usr/local/lib64/fftw/pgi/lib/libfftw3f.a -lm /usr/X11R6/lib64/libXm.so -lXmu -lSM -lICE -lXext -lXp -lXt -lX11 --rpath /usr/X11R6/lib64 --rpath /usr/X11R6/lib64 pgcc-Warning-Unknown switch: --rpath pgcc-Warning-Unknown switch: --rpath File with unknown suffix passed to linker: /usr/X11R6/lib64 File with unknown suffix passed to linker: /usr/X11R6/lib64 . . . I googled this kind of error, but it's only reported to LAM... in that case, they basically recomend to pass the -Wl flag to the linker. Did anybody here faced this problem before? How it was solved? And exactly how culd I pas that extra flag just to the linker (tried straight the LDFLAGS, then the ./configure does not find that the compiler can produce executables... :p )? Thanks you all for all the help. Promisse to send the results of the benchs to here when they are finished. :) Thanks again, JonesOn 4/20/06, Erik Lindahl [EMAIL PROTECTED] wrote: Hi,On Apr 20, 2006, at 12:25 PM, Ge Sunny wrote: Dear Florian, Thanks for your help. The installation of FFTW3 source code does work by setting the prefix. Then, I have set LDFLAGS and CPPFLAGS to install Gromacs from gromacs-3.3.1-1.src.rpm. However, there is an error when installing Gromacs: $ rpmbuild -rebuild gromacs-3.3.1-1.src.rpm ... ... checking for fftw3.h.. . yes checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library error: Bad exit status from /var/tmp/rpm-tmp.67043 (%build) RPM build errors:user erikli does not exist - using root group el does not exist - using rootuser erikli does not exist - using rootgroup el does not exist - using rootBad exit status from /var/tmp/rpm-tmp.67043 (%build) I can only find fftw3.f under ./fftw/include. Don't know what fftw3f is.The single precision FFTW3 library. You probably didn't include --enable-float. Go through the detailed instructions at http://www.gromacs.org/installation/prerequisites.phpCheers,Erik___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: PGI compilation error: --rpath problem?
Hi David. Well, I mentioned that change cause when compiling it with the PGI compiler the 3.3.1 version of gromacs yelded the exactly same error message: PGC-S-0090-Scalar data type required for logical expression (gmx_sgangle.c: ###) I just don't remember at this point the line number where the error appeared, despite knowing that this is just one line. I can retry the compilation with the original file and send the full error message to here later. So, was there any changes in that file since then? If so, I'm then stil locked in the error message above. :( For both single and double precision then. :( Any idea of what to do now? Anyway, thanks a lot for everything. Jones On 4/24/06, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Ok, thanks a lot. adding the wthout x and motif stuff in configure, plus the corrections for gmx_sgangle.c found at http://www.gromacs.org/pipermail/gmx-users/2005-December/018885.html made the compilation work. Now I'm having some strange problem: I am trying as test the mixed sample in the tutor directory. When trying it as is with the *double precision* version of gromacs I compiled, it yelds this error: . . If you mention that change, didn't you download the 3.3.1 version for this test? . step 0 Step 1 Warning: pressure scaling more than 1%, mu: 1.01018 1.02193 1.08117 Step 2 Warning: pressure scaling more than 1%, mu: 1.01124 1.00787 1.08362 Step 3 Warning: pressure scaling more than 1%, mu: 1.03039 1.0523 1.08046 Step 4 Warning: pressure scaling more than 1%, mu: 1.04141 1.08638 1.09351 Step 5 Warning: pressure scaling more than 1%, mu: 1.06415 1.0995 1.06772 Step 6 Warning: pressure scaling more than 1%, mu: 1.04802 1.07721 1.04162 Step 7 Warning: pressure scaling more than 1%, mu: 1.02981 1.03652 1.01836 Step 8 Warning: pressure scaling more than 1%, mu: 1.01626 1.01848 1.00881 Step 9 Warning: pressure scaling more than 1%, mu: 1.01081 1.01178 1.00552 step 130, remaining runtime: 0 s Step 140 Warning: pressure scaling more than 1%, mu: 1.00411 1.00022 1.0102 step 140, remaining runtime: 0 s Step 141 Warning: pressure scaling more than 1%, mu: 1.00439 1.00019 1.01173 Step 142 Warning: pressure scaling more than 1%, mu: 1.00395 1.00019 1.01172 Step 143 Warning: pressure scaling more than 1%, mu: 1.00304 1.00017 1.01009 step 240, remaining runtime: 0 s --- Program mdrun_d, VERSION 3.3 Source code file: stat.c, line: 283 Fatal error: XTC error --- Fly to the Court of England and Unfold (Macbeth, Act 3, Scene 6, William Shakespeare) And dies at this point. When using the single precision gromacs, it seems to runs smoothly. :) Same for both single and double precision compiled with gcc. Anyone got this kind of stuff before? Thanks a lot! :D On 4/24/06, *David van der Spoel* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi all! Ok, I did not acquired to compile gromacs with intel yet, but now I'm also facing problems with PGI compilers (which also has the extra problem of needin to be redownloaded soon). Just in case someone asks: I'm trying to benchmark gromacs in A64s with different compilers. ;) Well, PGI is dieing here: . . . /usr/local/pgi/linux86-64/6.0 /bin/pgcc -tp=k8-64 -fastsse -Mipa=fast -Mipa=inline -o grompp topio.o toppush.o topcat.o topshake.o convparm.o tomorse.o sorting.o splitter.o vsite_parm.o readir.o add_par.o topexcl.o toputil.o topdirs.o grompp.o -L/usr/local/lib64/fftw/pgi/lib ../mdlib/.libs/libmd.a -L/usr/X11R6/lib64 -L/usr/X11/lib ../gmxlib/.libs/libgmx.a -lnsl /usr/local/lib64/fftw/pgi/lib/libfftw3f.a -lm /usr/X11R6/lib64/libXm.so -lXmu -lSM -lICE -lXext -lXp -lXt -lX11 --rpath /usr/X11R6/lib64 --rpath /usr/X11R6/lib64 pgcc-Warning-Unknown switch: --rpath pgcc-Warning-Unknown switch: --rpath File with unknown suffix passed to linker: /usr/X11R6/lib64 File with unknown suffix passed to linker: /usr/X11R6/lib64 . try compiling without X windows in that case. . . I googled this kind of error, but it's only reported to LAM... in that case, they basically recomend to pass the -Wl flag to the linker. Did anybody here faced this problem before? How it was solved? And exactly how culd I pas that extra flag just to the linker (tried straight the LDFLAGS, then the ./configure does not find that the compiler can produce executables... :p )? Thanks you all for all the help
Re: [gmx-users] PGI compilation error: --rpath problem?
Hi all. Well, if I do not use the clue provided in http://www.gromacs.org/pipermail/gmx-users/2005-December/018885.html, I end up in the following error: . . . source='gmx_sgangle.c' object='gmx_sgangle.lo' libtool=yes \ DEPDIR=.deps depmode=none /bin/sh ../../config/depcomp \ /bin/sh ../../libtool --mode=compile --tag=CC /usr/local/pgi/linux86-64/6.0/bin/pgcc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\/usr/local/bin/chemistry/gromacs/PSI//share/top\ -I/usr/local/lib64/fftw/pgi/include -tp=k8-64 -fastsse -Mipa=fast -Mipa=inline -c -o gmx_sgangle.lo gmx_sgangle.c /usr/local/pgi/linux86-64/6.0/bin/pgcc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\/usr/local/bin/chemistry/gromacs/PSI//share/top\ -I/usr/local/lib64/fftw/pgi/include -tp=k8-64 -fastsse -Mipa=fast -Mipa=inline -c gmx_sgangle.c -o gmx_sgangle.o PGC-S-0090-Scalar data type required for logical _expression_ (gmx_sgangle.c: 313) PGC-S-0090-Scalar data type required for logical _expression_ (gmx_sgangle.c: 320) PGC/x86-64 Linux/x86-64 6.0-5: compilation completed with severe errors make[3]: ** [gmx_sgangle.lo] Erro 1 make[3]: Leaving directory `/home/johannes/src/gromacs/gromacs-3.3/src/tools' make[2]: ** [all-recursive] Erro 1 make[2]: Leaving directory `/home/johannes/src/gromacs/gromacs-3.3/src' make[1]: ** [all] Erro 2 make[1]: Leaving directory `/home/johannes/src/gromacs/gromacs-3.3/src' make: ** [all-recursive] Erro 1 . On the other hand, using that modified version of the gmx_sgangle.c ended up in errors when using the double precision version of gromacs (I'm using the 3.1.1 version) to run the mixed test simulation from tutor directory: . . . step 0 Step 1Warning: pressure scaling more than 1%, mu: 1.01018 1.02193 1.08117 Step 2Warning: pressure scaling more than 1%, mu: 1.01124 1.00787 1.08362 Step 3Warning: pressure scaling more than 1%, mu: 1.03039 1.0523 1.08046 Step 4Warning: pressure scaling more than 1%, mu: 1.04141 1.08638 1.09351 Step 5Warning: pressure scaling more than 1%, mu: 1.06415 1.0995 1.06772 Step 6Warning: pressure scaling more than 1%, mu: 1.04802 1.07721 1.04162 Step 7Warning: pressure scaling more than 1%, mu: 1.02981 1.03652 1.01836 Step 8Warning: pressure scaling more than 1%, mu: 1.01626 1.01848 1.00881 Step 9Warning: pressure scaling more than 1%, mu: 1.01081 1.01178 1.00552 step 130, remaining runtime: 0 s Step 140Warning: pressure scaling more than 1%, mu: 1.00411 1.00022 1.0102 step 140, remaining runtime: 0 s Step 141Warning: pressure scaling more than 1%, mu: 1.00439 1.00019 1.01173 Step 142Warning: pressure scaling more than 1%, mu: 1.00395 1.00019 1.01172 Step 143Warning: pressure scaling more than 1%, mu: 1.00304 1.00017 1.01009 step 240, remaining runtime: 0 s --- Program mdrun_d, VERSION 3.3 Source code file: stat.c, line: 283 Fatal error: XTC error --- Fly to the Court of England and Unfold (Macbeth, Act 3, Scene 6, William Shakespeare). Finally, it behaves like that while using the PGI compilers. It works properly with GCC. Any ideas of where to go now? :( Thanks for everything. JonesOn 4/24/06, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Ok, thanks a lot. adding the wthout x and motif stuff in configure, plus the corrections for gmx_sgangle.c found at http://www.gromacs.org/pipermail/gmx-users/2005-December/018885.html made the compilation work. Now I'm having some strange problem: I am trying as test the mixed sample in the tutor directory. When trying it as is with the *double precision* version of gromacs I compiled, it yelds this error: . .If you mention that change, didn't you download the 3.3.1 version forthis test? . step 0 Step 1Warning: pressure scaling more than 1%, mu: 1.01018 1.02193 1.08117 Step 2Warning: pressure scaling more than 1%, mu: 1.01124 1.00787 1.08362 Step 3Warning: pressure scaling more than 1%, mu: 1.03039 1.0523 1.08046 Step 4Warning: pressure scaling more than 1%, mu: 1.04141 1.08638 1.09351 Step 5Warning: pressure scaling more than 1%, mu: 1.06415 1.0995 1.06772 Step 6Warning: pressure scaling more than 1%, mu: 1.04802 1.07721 1.04162 Step 7Warning: pressure scaling more than 1%, mu: 1.02981 1.03652 1.01836 Step 8Warning: pressure scaling more than 1%, mu: 1.01626 1.01848 1.00881 Step 9Warning: pressure scaling more than 1%, mu: 1.01081 1.01178 1.00552 step 130, remaining runtime: 0 s Step 140Warning: pressure scaling more than 1%, mu: 1.00411 1.00022 1.0102 step 140, remaining runtime: 0 s Step 141Warning: pressure scaling more than 1%, mu: 1.00439 1.00019 1.01173 Step 142Warning: pressure scaling more than 1%, mu: 1.00395 1.00019 1.01172 Step 143Warning: pressure scaling more than 1%, mu: 1.00304 1.00017 1.01009 step 240, remaining runtime: 0 s --- Program mdrun_d, VERSION 3.3 Source code file: stat.c, line: 283 Fatal error
