[gmx-users] is it possible?
Hello: I've got two polar residues which make H-bond directly. However, I found that this Hbond can be broken by solvent molecules: sometimes there is 1 water molecule stucked in the middle during the simulation and sometimes 2 even 3. But those water molecules can bridge this two residues through Hbonds. So I am just wondering is it possible in Gromacs to make statstics on the number of water molecule stuck within this two residues? thank you very much. Albert -- 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] Re: Potential energy from a previous configuration mismatch
Thanks for the tip about nstlist, I will make good use of it. I also tried the NPT and the NVT ensembles with different temperatures and pressures, and I always had blow-up and large energies. Now I tried decreasing the time step up to 10 times, but still have blow-up problem and the potential energy at the start of the MD is 1E10 times larger that after minimization. Most often the contraints give problems, but I have read that it is normal and it makes sense. Just in case, I tried different lincs parameters, and also shake instead, but always with the same result. Is there any other thing I can check? Thanks for your advice -- View this message in context: http://gromacs.5086.n6.nabble.com/Potential-energy-from-a-previous-configuration-mismatch-tp5003352p5003385.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] is it possible?
Not easily - a complex geometric criterion is needed to define a multi-molecule H-bonding bridge. g_hbond can probably be made to do the simple case with 1 bridging water, but anything more complex than that will need the functionality of g_select. Mark On Fri, Nov 30, 2012 at 10:31 AM, Albert mailmd2...@gmail.com wrote: Hello: I've got two polar residues which make H-bond directly. However, I found that this Hbond can be broken by solvent molecules: sometimes there is 1 water molecule stucked in the middle during the simulation and sometimes 2 even 3. But those water molecules can bridge this two residues through Hbonds. So I am just wondering is it possible in Gromacs to make statstics on the number of water molecule stuck within this two residues? thank you very much. Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Build on OSX with 4.6beta1
Dear All, I have successfully compiled the beta1 of gromacs 4.6 on my macbook pro with mountain lion. I used the latest cuda and the clang/clang++ compilers in order to have access to the AVX instructions. mdrun works with great performances!! great job! two things: 1. the compilation was easy but not straightforward: cmake ../ -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/Users/carlo/Codes/gromacs-4.6/build-gpu -DCMAKE_CXX_COMPILER=/usr/bin/clang++ -DCMAKE_C_COMPILER=/usr/bin/clang -DCUDA_NVCC_HOST_COMPILER=/usr/bin/gcc -DCUDA_PROPAGATE_HOST_FLAGS=OFF and then I had to manually edit src/gmxlib/CMakeFiles/gmx.dir/link.txt and change clang to clang++ (I noted that in many other places it was correctly set, and without this change I got an error on some c++ related stuff) 2. is there any way to have openmp parallelisation on osx? Best, Carlo -- 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] mixed single-precision GPU and double-precision CPU calculation
Hi, As the new Verlet cut-off scheme, also used on the GPU, uses separate non-bonded coordinate and force buffers, implementing this will require very little code changes. All real variables in the nbnxn_atomdata_t data structure and in all code operating on them should be replaced by floats. We might implement this, but currently we are far too busy with other things. Cheers, Berk From: makoto-yon...@aist.go.jp To: gmx-users@gromacs.org Date: Thu, 29 Nov 2012 09:37:41 +0900 Subject: [gmx-users] mixed single-precision GPU and double-precision CPU calculation Dear GROMACS peoples: I know the current gromacs-4.6 can't build with both GPU and double precision being enable. I'm wondering is it possible to modify mixed single-precision (non-bonded) GPU calculation and double-precision CPU calculation? I suppose this combination would be practically useful when we needs high precision constraint calculation (with SHAKE or LINCS etc.). If it is possible by modifying some routine, please teach me the routine to modify. I would like to try it. Thank you for advance. Makoto Yoneya, Dr. AIST, Japan Makoto Yoneya, Dr. http://staff.aist.go.jp/makoto-yoneya/ -- gmx-users mailing list gmx-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] Observations about g_hbond -dist and -ang
Hi everyone, Ithought I should share something that I've noticed about some of the outputs of g_hbond, in case it's confused anyone else. I'd noticed that there is a significant difference in the length distribution plots (-dist) produced by version 3.3.3 and all of the 4 family, including 4.5.5 (which I believe included a bugfix for g_hbond). I then figured out that this difference is really just a problem with the .xvg legends. In 3.3.3 the distribution values were calculated for Hydrogen - Acceptor Distance (nm) and this description is still provided in the legend for 4.5.5, even though the values provided now are actually Donor - Acceptor Distance (nm). If you use -noda in 4.5.5 it will give you an identical distribution to 3.3.3. I then realised that both versions also have the angle distribution plots (-ang) labelled wrongly with Donor - Hydrogen - Acceptor Angle (\SO\N) instead of Hydrogen - Donor - Acceptor Angle. I'm not sure if these things would really be considered bugs, but I just thought I'd let people know. Cara -- 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] Build on OSX with 4.6beta1
On Fri, Nov 30, 2012 at 5:01 AM, Carlo Camilloni carlo.camill...@gmail.comwrote: Dear All, I have successfully compiled the beta1 of gromacs 4.6 on my macbook pro with mountain lion. I used the latest cuda and the clang/clang++ compilers in order to have access to the AVX instructions. mdrun works with great performances!! great job! two things: 1. the compilation was easy but not straightforward: cmake ../ -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/Users/carlo/Codes/gromacs-4.6/build-gpu -DCMAKE_CXX_COMPILER=/usr/bin/clang++ -DCMAKE_C_COMPILER=/usr/bin/clang -DCUDA_NVCC_HOST_COMPILER=/usr/bin/gcc -DCUDA_PROPAGATE_HOST_FLAGS=OFF and then I had to manually edit src/gmxlib/CMakeFiles/gmx.dir/link.txt and change clang to clang++ (I noted that in many other places it was correctly set, and without this change I got an error on some c++ related stuff) If you have git, does the version you get from: git init gromacs.dev cd gromacs.dev git fetch https://gerrit.gromacs.org/gromacs refs/changes/54/1854/1 git checkout FETCH_HEAD fix this issue? 2. is there any way to have openmp parallelisation on osx? As far as I know you have two options: - You can get the none free Intel ICC. - You can use gcc (ideally 4.7). I have tried only the one from MacPorts. But the version from MacPorts uses an assembler which doesn't support AVX. You need to work around that as described here: http://old.nabble.com/Re%3a-gcc,-as,-AVX,-binutils-and-MacOS-X-10.7-p32584737.htmlFor more details see http://redmine.gromacs.org/issues/1021 Roland Best, Carlo -- 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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] Build problem with 4.6beta1
On 11/29/12 10:25 PM, Szilárd Páll wrote: On Fri, Nov 30, 2012 at 3:20 AM, Justin Lemkul jalem...@vt.edu wrote: Hooray for being the first to report a problem with the beta :) We have a cluster at our university that provides us with access to some CPU-only nodes and some CPU-GPU nodes. I'm having problems with getting 4.6beta1 to build, and I suspect the issue is related to GPU detection. Here are some specifics: FFTW 3.3.3 CMake 2.8.10 gcc 4.3.4 CUDA 4.0 64-bit Linux on AMD hardware GPU nodes have Tesla C2050 cards Note that on AMD you might have to use less threads per process than the default and therefore more than one process per GPU: set -gpu_id=00 for two processes in a node to both use the first GPU. Additionally, you might want to use a newer gcc and CUDA, both will provide performance improvements. Thanks for the tips. I may be able to get the sysadmins to install a newer gcc, but I've already been told that CUDA can't be upgraded past 4.0, for a variety of technical reasons that I quite honestly don't understand. Commands: cmake ../gromacs-4.6-beta1 -DCMAKE_INSTALL_PREFIX=/home/** jalemkul/software/gromacs-**46beta1 -DGMX_X11=OFF -DGMX_GPU=ON -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_PREFIX_PATH=/home/ **jalemkul/software/fftw-3.3.3/ The first step runs alright, but two things to note: 1. It doesn't detect any GPU, which is correct because I'm on a head node and not a compute node: ...-- Looking for NVIDIA GPUs present in the system -- Could not detect NVIDIA GPUs -- Found CUDA: /cm/shared/apps/cuda40/**toolkit/4.0.17 (found suitable version 4.0, minimum required is 3.2) ... That is just an informative message. We try to detect GPUs on the build machine to suggest users compiling with GPU acceleration enabled. OK, I just wanted to make sure this wouldn't be an issue. 2. It says FFTW isn't detected, but it actually is: ... -- checking for module 'fftw3f' -- package 'fftw3f' not found -- Looking for fftwf_plan_r2r_1d in /home/jalemkul/ATHENA/** software/fftw-3.3.3/lib/**libfftw3f.so -- Looking for fftwf_plan_r2r_1d in /home/jalemkul/ATHENA/** software/fftw-3.3.3/lib/**libfftw3f.so - found -- Looking for fftwf_have_simd_avx in /home/jalemkul/ATHENA/** software/fftw-3.3.3/lib/**libfftw3f.so -- Looking for fftwf_have_simd_avx in /home/jalemkul/ATHENA/** software/fftw-3.3.3/lib/**libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /home/jalemkul/ATHENA/** software/fftw-3.3.3/lib/**libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /home/jalemkul/ATHENA/** software/fftw-3.3.3/lib/**libfftw3f.so - found ... Upon running make, I get an immediate failure: [ 0%] Building NVCC (Device) object src/gmxlib/gpu_utils/** CMakeFiles/gpu_utils.dir//./**gpu_utils_generated_gpu_utils.**cu.o nvcc fatal : redefinition of argument 'compiler-bindir' CMake Error at gpu_utils_generated_gpu_utils.**cu.o.cmake:206 (message): Error generating /home/jalemkul/gmxbuild/src/**gmxlib/gpu_utils/CMakeFiles/** gpu_utils.dir//./gpu_utils_**generated_gpu_utils.cu.o make[2]: *** [src/gmxlib/gpu_utils/**CMakeFiles/gpu_utils.dir/./** gpu_utils_generated_gpu_utils.**cu.o] Error 1 make[1]: *** [src/gmxlib/gpu_utils/**CMakeFiles/gpu_utils.dir/all] Error 2 make: *** [all] Error 2 That's bad and I don't exactly know why does it happen, it looks like the nvcc host compiler gets double-set. Could you put your CMakeCache.txt of this configuration into pastbin and link it (attachments are blocked, I think)? One option to get it work is to remove the -ccbin=/path/to/your/gcc form the CUDA_NVCC_FLAGS cache variable and re-configure. I can try to play around with it a little more later today, though it seems like simply using a pre-2.8.10 version of CMake does the trick. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://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] Re: Potential energy from a previous configuration mismatch
On 11/30/12 4:45 AM, escajarro wrote: Thanks for the tip about nstlist, I will make good use of it. I also tried the NPT and the NVT ensembles with different temperatures and pressures, and I always had blow-up and large energies. Now I tried decreasing the time step up to 10 times, but still have blow-up problem and the potential energy at the start of the MD is 1E10 times larger that after minimization. Most often the contraints give problems, but I have read that it is normal and it makes sense. Just in case, I tried different lincs parameters, and also shake instead, but always with the same result. Is there any other thing I can check? It's strange that you're getting constraint problems when your .mdp file specifies no constraints. You also have no bond energy term in the .log file, so it suggests that somehow constraints are actually being used. Are they explicitly defined in the topology? Is your geometry sensible after EM? The only thing I can really think of is that the minimization without constraints led to some kind of distorted geometry that, upon initiation of any dynamics, simply fails. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://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] Observations about g_hbond -dist and -ang
30 nov 2012 kl. 12.24 skrev Cara Kreck: Hi everyone, Ithought I should share something that I've noticed about some of the outputs of g_hbond, in case it's confused anyone else. I'd noticed that there is a significant difference in the length distribution plots (-dist) produced by version 3.3.3 and all of the 4 family, including 4.5.5 (which I believe included a bugfix for g_hbond). I then figured out that this difference is really just a problem with the .xvg legends. In 3.3.3 the distribution values were calculated for Hydrogen - Acceptor Distance (nm) and this description is still provided in the legend for 4.5.5, even though the values provided now are actually Donor - Acceptor Distance (nm). If you use -noda in 4.5.5 it will give you an identical distribution to 3.3.3. I then realised that both versions also have the angle distribution plots (-ang) labelled wrongly with Donor - Hydrogen - Acceptor Angle (\SO\N) instead of Hydrogen - Donor - Acceptor Angle. I'm not sure if these things would really be considered bugs, but I just thought I'd let people know. Thanks for pointing it out. I'd call it a bug, but a low priority one. Would you mind filing a redmine issue about it (http://redmine.gromacs.org/projects/gromacs/issues)? Then this will be much less likely to be overlooked or forgotten about. Erik Cara -- 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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] Re: Potential energy from a previous configuration mismatch
I do have constraints, all the bond lengths are fixed and they are specified in the topology file. Am I doing something wrong? I copy here the definition of one of the models I use. I also tried using in the input the line: constraints = all-bonds instead of constraints = none with the same result http://gromacs.5086.n6.nabble.com/file/n5003394/Clipboard.jpg -- View this message in context: http://gromacs.5086.n6.nabble.com/Potential-energy-from-a-previous-configuration-mismatch-tp5003352p5003394.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Electrostatic field in atoms - GROMACS is not reading table interaction functions for bonded interactions
Date: Thu, 29 Nov 2012 08:58:50 -0500 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Electrostatic field in atoms - GROMACS is not reading table interaction functions for bonded interactions On 11/29/12 8:18 AM, Ariana Torres Knoop wrote: Dear GROMACS users, We are trying to determine the electric fields at the C and N atoms in a protein. To do so, we thought of performing a one step energy minimization with the Lennard-Jones as well as the bonded interactions turned off, in order to get only the coulomb forces. For that, according to www.gromacs.org/Documentation/How-tos/Tabulated_Potentials , we made a table (table.xvg) in which the Lennard-Jones potential was set to zero and we also made three tables (table_b1.xvg, table_a5.xvg and table_d5.xvg) according to section 4.2.13 of the Manual (Tabulated interaction functions), in which the f(x)=0 for the whole range of distances, angles, dihedrals present in the simulation box. The numbers 1, 5, 2 correspond to the function number referred to in the topology file. For example for the bonds interaction, in the topology file we have: [ bonds ] ; ai aj funct c0 c1 c2 c3 1 2 1 1 3 1 1 4 1 1 5 1 5 6 1 . . . so we named the table table_b1.xvg. We changed the run.mdp file as follows: vdw-type = User coulombtype = PME-User And then we try to run it using: mdrun -v -deffnm run.tpr When checking the energy contribution using g_energy, Lennard-Jones contribution was indeed zero, but for the bonded interactions this is not the case: Energy Average Err.Est. RMSD Tot-Drift --- U-B 18180.1 -- 276.416 -540.638 (kJ/mol) Proper Dih. 11732.3 -- 27.6829 -54.0396 (kJ/mol) Improper Dih. 1027.26 -- 47.1598 -91.7097 (kJ/mol) LJ-14 0 -- 0 0 (kJ/mol) LJ (SR) 0 -- 0 0 (kJ/mol) We though that maybe the tables for the bonded interactions were not taken, so we tried: mdrun -v -tableb table_b1.xvg table_a5.xvg table_d2.xvg -deffnm run.tpr But it also did not work. We are not sure whether the problem is in the table definition, the way of running the program, the run type, the name of the tables, or if there should be some other modifications in the *mdp file. We would be very grateful if anyone could help us out here. I think the problem comes from the fact that the function types you are specifying in the topology correspond to actual potentials and thus the tables are being ignored. Per Table 5.5, it seems that any value for the table is acceptable (n = 0) but using numbers corresponding to actual function types may not work. The specified format also requires that both the table number and force constant (k) be specified in the topology, but the [bonds] section you show above has no value of k and the function type corresponds to a simple harmonic bond. There is no bond energy in the output, which suggests you are using constraints - is that the case? No, the issue is that you are using function type 1. Tabulated bonds are function type 8 or 9, that is what should be in the 3rd column. The actual number for the table file should appear after that in the 4th column. Cheers, Berk -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 list gmx-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] Build on OSX with 4.6beta1
Hi, On Fri, Nov 30, 2012 at 5:01 AM, Carlo Camilloni carlo.camill...@gmail.comwrote: 1. the compilation was easy but not straightforward: cmake ../ -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/Users/carlo/Codes/gromacs-4.6/build-gpu -DCMAKE_CXX_COMPILER=/usr/bin/clang++ -DCMAKE_C_COMPILER=/usr/bin/clang -DCUDA_NVCC_HOST_COMPILER=/usr/bin/gcc -DCUDA_PROPAGATE_HOST_FLAGS=OFF One more thing. Could you try whether the problem is fixed with -DCUDA_NVCC_HOST_COMPILER=/usr/bin/g++ ? Roland -- 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] Re: Potential energy from a previous configuration mismatch
On 11/30/12 8:21 AM, escajarro wrote: I do have constraints, all the bond lengths are fixed and they are specified in the topology file. Am I doing something wrong? I copy here the definition of one of the models I use. I also tried using in the input the line: constraints = all-bonds instead of constraints = none with the same result http://gromacs.5086.n6.nabble.com/file/n5003394/Clipboard.jpg That all looks fine, and the results should be the same under those two circumstances. The problem is likely due to the fact that L-BFGS cannot actually make use of constraints (a bug in mdrun), so that is the source of the difference. The EM is being done without constraints, and then the MD starts with constraints. Use a different EM algorithm and see if the outcome improves. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://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] RE: mixed single-precision GPU and double-precision CPU calculation
Dear Berk: Thanks a lot for your positive comments. I'm very happy the mixed calculation option will be realised in near future. Regards, Makoto -- View this message in context: http://gromacs.5086.n6.nabble.com/mixed-single-precision-GPU-and-double-precision-CPU-calculation-tp5003328p5003398.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] g_hbond routine
Dear gromacs users, in the Gromacs manual pages (version 4.5.3 page 211) there are the criteria to have an Hbond. r 0.35 nm, where r is the Donor-Acceptor distance alpha 30°, where alpha is the Hydrogen-Donor-Acceptor angle in the Manual page for g_hbond (version 4.5.3 page 275) it is written Hydrogen bonds are determined based on cutoffs for the angle Acceptor - Donor - Hydrogen (zero is extended) and the distance Hydrogen - Acceptor and even in the file that exits by using the option -dist the xaxis label is Hydrogen - Acceptor Distance (nm) but I think this is the Donor-Acceptor distance because it seems too big to be the Hydrogen-Acceptor distance. Which distance is it? Thank you very much, Velia -- 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] g_hbond routine
On 11/30/12 10:41 AM, Velia Minicozzi wrote: Dear gromacs users, in the Gromacs manual pages (version 4.5.3 page 211) there are the criteria to have an Hbond. r 0.35 nm, where r is the Donor-Acceptor distance alpha 30°, where alpha is the Hydrogen-Donor-Acceptor angle in the Manual page for g_hbond (version 4.5.3 page 275) it is written Hydrogen bonds are determined based on cutoffs for the angle Acceptor - Donor - Hydrogen (zero is extended) and the distance Hydrogen - Acceptor and even in the file that exits by using the option -dist the xaxis label is Hydrogen - Acceptor Distance (nm) but I think this is the Donor-Acceptor distance because it seems too big to be the Hydrogen-Acceptor distance. Which distance is it? It depends on what you select. You control whether it is the H-A or D-A distance using the -da flag. By default, it is a D-A distance. There is small output bug was reported this morning and there is an open Redmine issue for it. It is low-priority, but will be fixed sometime in the future. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://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] Build problem with 4.6beta1
On Fri, Nov 30, 2012 at 3:20 AM, Justin Lemkul jalem...@vt.edu wrote: Hooray for being the first to report a problem with the beta :) :) Thanks! We have a cluster at our university that provides us with access to some CPU-only nodes and some CPU-GPU nodes. I'm having problems with getting 4.6beta1 to build, and I suspect the issue is related to GPU detection. Here are some specifics: FFTW 3.3.3 CMake 2.8.10 gcc 4.3.4 CUDA 4.0 64-bit Linux on AMD hardware GPU nodes have Tesla C2050 cards Commands: cmake ../gromacs-4.6-beta1 -DCMAKE_INSTALL_PREFIX=/home/** jalemkul/software/gromacs-**46beta1 -DGMX_X11=OFF -DGMX_GPU=ON -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_PREFIX_PATH=/home/ **jalemkul/software/fftw-3.3.3/ The first step runs alright, but two things to note: 1. It doesn't detect any GPU, which is correct because I'm on a head node and not a compute node: Yes, but we try to be vigilant about looking for them - however there's not really an API to do that for unless you already have CUDA set up :-S. Need to work on our install guide here too - the detection applies to the node you're compiling on, but you can change that and compile however you like within the limits of the compiler. ...-- Looking for NVIDIA GPUs present in the system -- Could not detect NVIDIA GPUs -- Found CUDA: /cm/shared/apps/cuda40/**toolkit/4.0.17 (found suitable version 4.0, minimum required is 3.2) ... 2. It says FFTW isn't detected, but it actually is: Right. We try to use pkgconfig to help detect FFTW, but the former might not exist and the latter might exist independently of the database of the former. So we then do some independent checking (which succeeded in your case). I've made a fix that I expect will keep pkgconfig quiet about its failure, and thus not distract people :-). Mark ... -- checking for module 'fftw3f' -- package 'fftw3f' not found -- Looking for fftwf_plan_r2r_1d in /home/jalemkul/ATHENA/** software/fftw-3.3.3/lib/**libfftw3f.so -- Looking for fftwf_plan_r2r_1d in /home/jalemkul/ATHENA/** software/fftw-3.3.3/lib/**libfftw3f.so - found -- Looking for fftwf_have_simd_avx in /home/jalemkul/ATHENA/** software/fftw-3.3.3/lib/**libfftw3f.so -- Looking for fftwf_have_simd_avx in /home/jalemkul/ATHENA/** software/fftw-3.3.3/lib/**libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /home/jalemkul/ATHENA/** software/fftw-3.3.3/lib/**libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /home/jalemkul/ATHENA/** software/fftw-3.3.3/lib/**libfftw3f.so - found ... Upon running make, I get an immediate failure: [ 0%] Building NVCC (Device) object src/gmxlib/gpu_utils/** CMakeFiles/gpu_utils.dir//./**gpu_utils_generated_gpu_utils.**cu.o nvcc fatal : redefinition of argument 'compiler-bindir' CMake Error at gpu_utils_generated_gpu_utils.**cu.o.cmake:206 (message): Error generating /home/jalemkul/gmxbuild/src/**gmxlib/gpu_utils/CMakeFiles/** gpu_utils.dir//./gpu_utils_**generated_gpu_utils.cu.o make[2]: *** [src/gmxlib/gpu_utils/**CMakeFiles/gpu_utils.dir/./** gpu_utils_generated_gpu_utils.**cu.o] Error 1 make[1]: *** [src/gmxlib/gpu_utils/**CMakeFiles/gpu_utils.dir/all] Error 2 make: *** [all] Error 2 Any ideas? I'm guessing it's related to the GPU detection failing, because I can build on a workstation in our lab that has a C2075 card. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Re: Potential energy from a previous configuration mismatch
On Fri, Nov 30, 2012 at 2:35 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/30/12 8:21 AM, escajarro wrote: I do have constraints, all the bond lengths are fixed and they are specified in the topology file. Am I doing something wrong? I copy here the definition of one of the models I use. I also tried using in the input the line: constraints = all-bonds instead of constraints = none with the same result http://gromacs.5086.n6.**nabble.com/file/n5003394/**Clipboard.jpghttp://gromacs.5086.n6.nabble.com/file/n5003394/Clipboard.jpg That all looks fine, and the results should be the same under those two circumstances. The problem is likely due to the fact that L-BFGS cannot actually make use of constraints (a bug in mdrun), so that is the source of the difference. The EM is being done without constraints, and then the MD starts with constraints. Use a different EM algorithm and see if the outcome improves. If L-BFGS is silently not using the constraints, then I think that is a real bug and it would be good to report it so we might sometime fix it. Or maybe it's an undocumented feature we need to document? Which is it, please? Mark -- 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] Re: Potential energy from a previous configuration mismatch
On 11/30/12 11:00 AM, Mark Abraham wrote: On Fri, Nov 30, 2012 at 2:35 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/30/12 8:21 AM, escajarro wrote: I do have constraints, all the bond lengths are fixed and they are specified in the topology file. Am I doing something wrong? I copy here the definition of one of the models I use. I also tried using in the input the line: constraints = all-bonds instead of constraints = none with the same result http://gromacs.5086.n6.**nabble.com/file/n5003394/**Clipboard.jpghttp://gromacs.5086.n6.nabble.com/file/n5003394/Clipboard.jpg That all looks fine, and the results should be the same under those two circumstances. The problem is likely due to the fact that L-BFGS cannot actually make use of constraints (a bug in mdrun), so that is the source of the difference. The EM is being done without constraints, and then the MD starts with constraints. Use a different EM algorithm and see if the outcome improves. If L-BFGS is silently not using the constraints, then I think that is a real bug and it would be good to report it so we might sometime fix it. Or maybe it's an undocumented feature we need to document? Which is it, please? From the recent discussion, it seems that L-BFGS is silently ignoring the constraints, as Berk observed there is no check for this combination, which explained David's finding that bond lengths seem to vary randomly: http://lists.gromacs.org/pipermail/gmx-developers/2012-November/006433.html -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://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] COLVAR not printing
Dear All, I have copied and patched the plumed script plumed_gromacs-4.5.5.sh, given in the patches directory. But after doing that, while running some umbrella sampling it's not printing the COLVAR file, only the simple md is running there. So, can anyone help me in this regard? Thanks -- Tarak -- 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] Re: Potential energy from a previous configuration mismatch
Thanks. http://redmine.gromacs.org/issues/1053 created. Mark On Fri, Nov 30, 2012 at 5:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/30/12 11:00 AM, Mark Abraham wrote: On Fri, Nov 30, 2012 at 2:35 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/30/12 8:21 AM, escajarro wrote: I do have constraints, all the bond lengths are fixed and they are specified in the topology file. Am I doing something wrong? I copy here the definition of one of the models I use. I also tried using in the input the line: constraints = all-bonds instead of constraints = none with the same result http://gromacs.5086.n6.**nabb**le.com/file/n5003394/Clipboard.jpghttp://nabble.com/file/n5003394/**Clipboard.jpg http://gromacs.**5086.n6.nabble.com/file/**n5003394/Clipboard.jpghttp://gromacs.5086.n6.nabble.com/file/n5003394/Clipboard.jpg That all looks fine, and the results should be the same under those two circumstances. The problem is likely due to the fact that L-BFGS cannot actually make use of constraints (a bug in mdrun), so that is the source of the difference. The EM is being done without constraints, and then the MD starts with constraints. Use a different EM algorithm and see if the outcome improves. If L-BFGS is silently not using the constraints, then I think that is a real bug and it would be good to report it so we might sometime fix it. Or maybe it's an undocumented feature we need to document? Which is it, please? From the recent discussion, it seems that L-BFGS is silently ignoring the constraints, as Berk observed there is no check for this combination, which explained David's finding that bond lengths seem to vary randomly: http://lists.gromacs.org/**pipermail/gmx-developers/2012-** November/006433.htmlhttp://lists.gromacs.org/pipermail/gmx-developers/2012-November/006433.html -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Re: Build on OSX with 4.6beta1
Hi Roland, so, the problem is not fixed by changing to -DCUDA_NVCC_HOST_COMPILER=/usr/bin/g++ , I still have to change by hand clang to clang++ in that single link.txt file, while everything works fine by checking out the revision you suggested. Best, Carlo Message: 3 Date: Fri, 30 Nov 2012 08:34:24 -0500 From: Roland Schulz rol...@utk.edu Subject: Re: [gmx-users] Build on OSX with 4.6beta1 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: CAO2Twb=c0jyknirtm7o5gxvhvuserwczvcjheeow-3-ypxv...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi, On Fri, Nov 30, 2012 at 5:01 AM, Carlo Camilloni carlo.camill...@gmail.comwrote: 1. the compilation was easy but not straightforward: cmake ../ -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/Users/carlo/Codes/gromacs-4.6/build-gpu -DCMAKE_CXX_COMPILER=/usr/bin/clang++ -DCMAKE_C_COMPILER=/usr/bin/clang -DCUDA_NVCC_HOST_COMPILER=/usr/bin/gcc -DCUDA_PROPAGATE_HOST_FLAGS=OFF One more thing. Could you try whether the problem is fixed with -DCUDA_NVCC_HOST_COMPILER=/usr/bin/g++ ? Roland -- 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] Re: Build on OSX with 4.6beta1
Hi Carlo, thanks for the feedback! Roland On Fri, Nov 30, 2012 at 1:35 PM, Carlo Camilloni carlo.camill...@gmail.comwrote: Hi Roland, so, the problem is not fixed by changing to -DCUDA_NVCC_HOST_COMPILER=/usr/bin/g++ , I still have to change by hand clang to clang++ in that single link.txt file, while everything works fine by checking out the revision you suggested. Best, Carlo Message: 3 Date: Fri, 30 Nov 2012 08:34:24 -0500 From: Roland Schulz rol...@utk.edu Subject: Re: [gmx-users] Build on OSX with 4.6beta1 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: CAO2Twb= c0jyknirtm7o5gxvhvuserwczvcjheeow-3-ypxv...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi, On Fri, Nov 30, 2012 at 5:01 AM, Carlo Camilloni carlo.camill...@gmail.comwrote: 1. the compilation was easy but not straightforward: cmake ../ -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/Users/carlo/Codes/gromacs-4.6/build-gpu -DCMAKE_CXX_COMPILER=/usr/bin/clang++ -DCMAKE_C_COMPILER=/usr/bin/clang -DCUDA_NVCC_HOST_COMPILER=/usr/bin/gcc -DCUDA_PROPAGATE_HOST_FLAGS=OFF One more thing. Could you try whether the problem is fixed with -DCUDA_NVCC_HOST_COMPILER=/usr/bin/g++ ? Roland -- 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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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
