Re: [gmx-users] TPI Results differ in v4.5.7 and v4.6.1
Niels, Which force-field did you use? I guess an uncharged CH4 shouldn't be giving different results for TPI when changing coulomb... Actually, coulomb is turned off if there's no charge in the particles to insert, if I remember the code correctly. João On Mon, Jun 24, 2013 at 3:40 PM, Niels Müller u...@nielsm.de wrote: Hi João, Indeed your instinct seems to be good! When switching the Coulomb-Type to Cut-Off, there doesn't seem to be a difference between 4.6 and 4.5. Apparently its an issue with the PME sum. We will investigate further. Am 24.06.2013 um 14:42 schrieb João M. Damas jmda...@itqb.unl.pt: Niels, This is very interesting. At our group, a colleague of mine and I have also identified differences in the TPI integrator between 4.0.X and 4.5.X, but we still haven't had the time to report it properly, since we are using a slightly modified version of the TPI algorithm. Instinctively, we were attributing it to some different behaviours in the RF that are observed between those versions. We also know that the TPI algorithm began allowing PME treatment from 4.5.X onwards, so maybe there are some differences going on the electrostatics level? But, IIRC, no modifications to the TPI code were on the release notes from 4.5.X to 4.6.X... We'll try to find some time to report our findings as soon as possible. Maybe they are related. Best, João On Mon, Jun 24, 2013 at 10:19 AM, Niels Müller u...@nielsm.de wrote: Hi GMX Users, We are computing the chemical potential of different gas molecules in a polymer melt with the tpi integrator. The computations are done for CO2 and CH4. The previous computations were done with v4.5.5 or 4.5.7 and gave equal results. I recently switched to gromacs version 4.6.1, and the chemical potential computed by this version is shifted by a nearly constant factor, which is different for the two gas molecules. We are perplexed what causes this shift. Was there any change in the new version that affects the tpi integration? I will provide the mdp file we used below. The tpi integration is run on basis of the last 10 ns of a 30 ns NVT simulation with 'mdrun -rerun'. Best regards, Niels. # The mdp file: # ; VARIOUS PREPROCESSING OPTIONS cpp = cpp include= define = ; RUN CONTROL PARAMETERS integrator = tpi ; Start time and timestep in ps tinit= 0 dt = 0.001 nsteps = 100 ; For exact run continuation or redoing part of a run init_step= 0 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Temperature, friction coefficient (amu/ps) and random seed bd-fric = 0.5 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 100 emstep = 0.01 ; Max number of iterations in relax_shells niter= 20 ; Step size (1/ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 100 nstvout = 0 nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint= 100 ; Output frequency for energies to log file and energy file nstlog = 100 nstenergy= 100 ; Output frequency and precision for xtc file nstxtcout= 0 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist= 0.9 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = pme rcoulomb-switch = 0 rcoulomb = 0.9 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r= 1 ; Method for doing Van der Waals vdw-type
[gmx-users] g_energy units
Dear users, is the energy output from g_energy really in kJ/mol? As an example, I wanted to know which isoform of a protein forms the most stable dimer. I calculated the potential energy of the interaction between two monomers of the dimer and I got -2000 kJ/mol for one isoform and -4000 kJ/mol for the other. Shouldn't it be J/mol? If these values are really in kJ/mol, how can I interpret it in terms of molecular scale? -2000 or -4000 kJ/mol sure is a lot of energy for such scale, in which the energies are typically at the order or 10s of kJ/mol. I know I'm not accounting for the entropic effects, but I have never seen an entropy contribution in the scales of 1000 kJ/mol either... Is it the case as these energy values are somewhat arbitrary and I can only say that one isoform has 2x the interaction energy of the other? I know this is not a bad structure with high energy case. I have been wondering about the values from g_energy for quite a long time and I have seen it in many different systems. my calculation procedure was as follows: From a standard explicit solvent MD trajectory (md.trr) I extracted only the protein with trjconv, creating the file md_protein.trr. I used tpbconv to do the same with the md.tpr file, creating md_protein.tpr. Then I re-ran the MD over this trajectory with mdrun: mdrun -s md_protein.tpr -rerun md_protein.trr -deffnm protein. The potential energy of the dimer was extracted from the created protein.edr file. The same was made for both chains A and B using an index file created with make_ndx. The dimer interaction energy was calculated as Potential_AB - (Potential_A + Potential_B). Is this wrong? Any help would be greatly appreciated. Thank you in advance, Leandro Bortot -- 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_energy units
What (change in) free-energy difference are you trying to measure? How do these potential energy (differences) relate to them? Mark On Sat, Jun 29, 2013 at 7:13 PM, Leandro Bortot leandro@gmail.com wrote: Dear users, is the energy output from g_energy really in kJ/mol? As an example, I wanted to know which isoform of a protein forms the most stable dimer. I calculated the potential energy of the interaction between two monomers of the dimer and I got -2000 kJ/mol for one isoform and -4000 kJ/mol for the other. Shouldn't it be J/mol? If these values are really in kJ/mol, how can I interpret it in terms of molecular scale? -2000 or -4000 kJ/mol sure is a lot of energy for such scale, in which the energies are typically at the order or 10s of kJ/mol. I know I'm not accounting for the entropic effects, but I have never seen an entropy contribution in the scales of 1000 kJ/mol either... Is it the case as these energy values are somewhat arbitrary and I can only say that one isoform has 2x the interaction energy of the other? I know this is not a bad structure with high energy case. I have been wondering about the values from g_energy for quite a long time and I have seen it in many different systems. my calculation procedure was as follows: From a standard explicit solvent MD trajectory (md.trr) I extracted only the protein with trjconv, creating the file md_protein.trr. I used tpbconv to do the same with the md.tpr file, creating md_protein.tpr. Then I re-ran the MD over this trajectory with mdrun: mdrun -s md_protein.tpr -rerun md_protein.trr -deffnm protein. The potential energy of the dimer was extracted from the created protein.edr file. The same was made for both chains A and B using an index file created with make_ndx. The dimer interaction energy was calculated as Potential_AB - (Potential_A + Potential_B). Is this wrong? Any help would be greatly appreciated. Thank you in advance, Leandro Bortot -- 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] Installation on Ubuntu 12.04LTS
Thanks guys! I think it's working now. Just in case others may run into the same difficulties, I am summarizing below what worked for me. I installed both gcc-4.4 and gcc-4.7 from synaptic. Then updated CUDA to 5.0, with the package cuda_5.0.35_linux_64_ubuntu11.10-1.run available from the nvidia site. Compiling cuda toolkit will require gcc-4.4, so I had to temporarily change some links: sudo ln -s /usr/bin/gcc-4.4 /usr/bin/gcc sudo ln -s /usr/bin/g++-4.4 /usr/bin/g++ Then I installed the toolkit and the samples: sudo ./cuda_5.0.35_linux_64_ubuntu11.10-1.run -toolkit Installing the CUDA samples required some extra packages on my system: sudo apt-get install freeglut3 sudo ln -s /usr/lib/x86_64-linux-gnu/libglut.so.3 /usr/lib/libglut.so sudo ./cuda_5.0.35_linux_64_ubuntu11.10-1.run -samples Then update my .bashrc: export LD_LIBRARY_PATH=/usr/local/cuda-5.0/lib64/:/usr/local/cuda-5.0/lib:$LD_LIBRARY_PATH export PATH=/usr/local/cuda-5.0/bin/:$PATH Finally confirm that CUDA 5.0 is the defoult compiler: nvcc -version Now I changed back the gcc links to install gromacs: sudo ln -s /usr/bin/gcc-4.7 /usr/bin/gcc sudo ln -s /usr/bin/g++-4.7 /usr/bin/g++ CUDA apparently check which gcc version is used, and will complain for gcc version above 4.6. Gromacs on the other end will require gcc-4.7. I found a solution on a blog, and comment out the compiler-check in the CUDA header file /usr/local/cuda-5.0/include/host_config.h Comment out: //#if __GNUC__ 4 || (__GNUC__ == 4 __GNUC_MINOR__ 6) //#error -- unsupported GNU version! gcc 4.7 and up are not supported! //#endif /* __GNUC__ 4 || (__GNUC__ == 4 __GNUC_MINOR__ 6) */ Now I could cmake/make/install gromacs: cmake .. -DGMX_GPU=ON -DGMX_BUILD_OWN_FFTW=ON make sudo make install And add the /usr/local/gromacs/bin/ directory to my path. I am still trying to fix the issues with the intel compiler. The gcc compiled version benchmark at 52ns/day with the lysozyme in water tutorial. Thanks again. From: Szilárd Páll szilard.p...@cbr.su.se To: Mare Libero marelibe...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, June 27, 2013 10:47 AM Subject: Re: [gmx-users] Installation on Ubuntu 12.04LTS On Thu, Jun 27, 2013 at 12:57 PM, Mare Libero marelibe...@yahoo.com wrote: Hello everybody, Does anyone have any recommendation regarding the installation of gromacs 4.6 on Ubuntu 12.04? I have the nvidia-cuda-toolkit that comes in synaptic (4.0.17-3ubuntu0.1 installed in /usr/lib/nvidia-cuda-toolkit) and the drivers 304.88. Apparently, this is not compatible with gcc-4.5 and higher. When I issue: $ cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit -DGMX_BUILD_OWN_FFTW=ON $ make the compilation ends with: In file included from /usr/lib/nvidia-cuda-toolkit/include/cuda_runtime.h:59:0, from command-line:0: /usr/include/host_config.h:82:2: error: #error -- unsupported GNU version! gcc 4.5 and up are not supported! If I downgrade to gcc-4.4 this error disappears, but gromacs compilation fails with a different error: cc1plus: error: unrecognized command line option -fexcess-precision=fast CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:198 (message): Error generating /home/me/Downloads/gromacs-4.6.2/build/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 I guess what happens is that you are using gcc 4.5 for the CPU code and gcc 4.4 as the nvcc host compiler. However, the compiler options used for gcc (CMAKE_CXX_FLAGS) get propagated to nvcc; -fexcess-precision=fast is supported by gcc 4.5, but not by 4.4, hence the error when compiling CUDA code. Also, I tried the Intel compilers that comes with the non-commercial Intel c++ composer XE (which I believe are recommended). The compilation produces a number of warnings, and then dies with the following error: $ CC=/opt/intel/bin/icc cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit -DGMX_BUILD_OWN_FFTW=ON [ 63%] Building C object share/template/CMakeFiles/template.dir/template.c.o make[2]: *** No rule to make target `src/gmxlib/libgmx.so.8', needed by `share/template/template'. Stop. make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 make: *** [all] Error 2 This should work, but CUDA 4.0 is ancient surely does not support icc 13. I suggest that you get CUDA 5.0 and use gcc 4.7 (or a new icc). If you really want to stick to CUDA 4.0, try using gcc 4.4 as the general C++ compiler (CMAKE_CXX_COMPILER) which should avoid the above error. Thanks in advance for your help, Al -- gmx-users mailing list gmx-users@gromacs.org
