[gmx-users] clarification regarding contact map - g_mdmat
Dear users, I used g_mdmap to calculate the C-alpha contact map of the trajectory. the distance cut off of 8.0 Ang was selected The protein is a dimer of 237 residues. The output of -no was like this - #resratio tot mean natm mean/atm 1 1.000 473 473.0001 473.000 2 1.000 473 473.0001 473.000 3 1.000 473 473.0001 473.000 4 1.000 473 473.0001 473.000 5 1.000 473 473.0001 473.000 6 1.000 473 473.0001 473.000 7 1.000 473 473.0001 473.000 So it mean that on an average each calpha atom contacts all other C-alpha atom in the whole trajectory at some point of time. In order to cross check it I collected data only for one time frame. This was also very similar results. all the residues have a minimum of atleast 471 contacts. Some one kindly clarify where I am going wrong.? the command I used was - g_mdmat -f .*.xtc -s *.tpr -no *.xvg -mean *.xpm -b 4000 -e 4000 -t 8.0 Is this trucating distance in Angstroms or nanometer? Thank you Kavya -- 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] grimaces 4.6 installation error
Here's the complete log file: https://dl.dropbox.com/u/11027999/make.log Thanks in advance. Fernando. On Jan 31, 2013, at 10:05 PM, Roland Schulz wrote: > On Thu, Jan 31, 2013 at 8:18 PM, Fernando Favela > wrote: > >> Dear Gromacs users, >> >> I'm trying to install GMX 4.6 in a 64 Bit Machine with Nvidia GTX 680 >> cards, I've already installed the intel compilers, cuda 5 and openmpi. >> >> I do the following procedure: >> CC=/opt/intel/bin/icc CXX=/opt/intel/bin/icpc cmake .. >> >> then >> >> sudo make -j 12 >> >> and I get this error: >> >> Linking CXX shared library libmd.so >> cd /home/ffavela/Downloads/gromacs-4.6/build-cmake/src/mdlib && >> /usr/bin/cmake -E cmake_link_script CMakeFiles/md.dir/link.txt --verbose=1 >> /opt/intel/bin/icpc -fPIC -mavx -Wall -ip -funroll-all-loops -O3 -DNDEBUG >> -shared -Wl,-soname,libmd.so.6 -o libmd.so.6 >> CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_gpu_ref.c.o >> CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_simd_4xn.c.o >> CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_common.c.o >> CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_simd_2xnn.c.o >> CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_ref.c.o >> CMakeFiles/md.dir/genborn_allvsall.c.o CMakeFiles/md.dir/qm_mopac.c.o >> CMakeFiles/md.dir/mvxvf.c.o CMakeFiles/md.dir/genborn.c.o >> CMakeFiles/md.dir/ebin.c.o CMakeFiles/md.dir/csettle.c.o >> CMakeFiles/md.dir/genborn_allvsall_sse2_single.c.o >> CMakeFiles/md.dir/pme.c.o CMakeFiles/md.dir/gmx_fft.c.o >> CMakeFiles/md.dir/force.c.o CMakeFiles/md.dir/qm_gaussian.c.o >> CMakeFiles/md.dir/qm_orca.c.o CMakeFiles/md.dir/mdatom.c.o >> CMakeFiles/md.dir/stat.c.o CMakeFiles/md.dir/perf_est.c.o >> CMakeFiles/md.dir/domdec_network.c.o CMakeFiles/md.dir/pme_pp.c.o >> CMakeFiles/md.dir/calcmu.c.o CMakeFiles/md.dir/shakef.c.o >> CMakeFiles/md.dir/fft5d.c.o CMakeFiles/md.dir/tables.c.o >> CMakeFiles/md.dir/qmmm.c.o CMakeFiles/md.dir/domdec_con.c.o >> CMakeFiles/md.dir/clincs.c.o CMakeFiles/md.dir/domdec_setup.c.o >> CMakeFiles/md.dir/gmx_wallcycle.c.o CMakeFiles/md.dir/gmx_fft_fftw3.c.o >> CMakeFiles/md.dir/partdec.c.o CMakeFiles/md.dir/domdec.c.o >> CMakeFiles/md.dir/genborn_allvsall_sse2_double.c.o >> CMakeFiles/md.dir/md_support.c.o CMakeFiles/md.dir/vsite.c.o >> CMakeFiles/md.dir/groupcoord.c.o CMakeFiles/md.dir/mdebin.c.o >> CMakeFiles/md.dir/gmx_fft_fftpack.c.o CMakeFiles/md.dir/tgroup.c.o >> CMakeFiles/md.dir/vcm.c.o CMakeFiles/md.dir/nsgrid.c.o >> CMakeFiles/md.dir/nbnxn_search.c.o CMakeFiles/md.dir/constr.c.o >> CMakeFiles/md.dir/shellfc.c.o CMakeFiles/md.dir/iteratedconstraints.c.o >> CMakeFiles/md.dir/rf_util.c.o CMakeFiles/md.dir/update.c.o >> CMakeFiles/md.dir/genborn_sse2_double.c.o CMakeFiles/md.dir/forcerec.c.o >> CMakeFiles/md.dir/nbnxn_atomdata.c.o >> CMakeFiles/md.dir/genborn_sse2_single.c.o CMakeFiles/md.dir/gmx_fft_mkl.c.o >> CMakeFiles/md.dir/pull.c.o CMakeFiles/md.dir/domdec_box.c.o >> CMakeFiles/md.dir/domdec_top.c.o CMakeFiles/md.dir/mdebin_bar.c.o >> CMakeFiles/md.dir/nlistheuristics.c.o CMakeFiles/md.dir/qm_gamess.c.o >> CMakeFiles/md.dir/coupling.c.o CMakeFiles/md.dir/adress.c.o >> CMakeFiles/md.dir/init.c.o CMakeFiles/md.dir/wnblist.c.o >> CMakeFiles/md.dir/expanded.c.o CMakeFiles/md.dir/wall.c.o >> CMakeFiles/md.dir/ns.c.o CMakeFiles/md.dir/minimize.c.o >> CMakeFiles/md.dir/sim_util.c.o CMakeFiles/md.dir/pullutil.c.o >> CMakeFiles/md.dir/gmx_parallel_3dfft.c.o CMakeFiles/md.dir/edsam.c.o >> CMakeFiles/md.dir/pull_rotation.c.o CMakeFiles/md.dir/gmx_fft_acml.c.o >> CMakeFiles/md.dir/tpi.c.o CMakeFiles/md.dir/ewald.c.o >> CMakeFiles/md.dir/calcvir.c.o nbnxn_cuda/libnbnxn_cuda.a >> ../gmxlib/libgmx.so.6 /usr/lib/libblas.so.3gf /usr/lib/liblapack.so.3gf >> /usr/lib/libblas.so.3gf -ldl -lm -lfftw3f -openmp /usr/lib/liblapack.so.3gf >> -ldl -lm -lfftw3f ../gmxlib/gpu_utils/libgpu_utils.a >> ../gmxlib/cuda_tools/libcuda_tools.a /usr/local/cuda/lib64/libcudart.so >> -lcuda -lpthread >> -Wl,-rpath,/home/ffavela/Downloads/gromacs-4.6/build-cmake/src/gmxlib:/usr/local/cuda/lib64: >> cd /home/ffavela/Downloads/gromacs-4.6/build-cmake/src/mdlib && >> /usr/bin/cmake -E cmake_symlink_library libmd.so.6 libmd.so.6 libmd.so >> make[2]: Leaving directory >> `/home/ffavela/Downloads/gromacs-4.6/build-cmake' >> /usr/bin/cmake -E cmake_progress_report >> /home/ffavela/Downloads/gromacs-4.6/build-cmake/CMakeFiles 89 90 91 92 93 >> 94 95 96 97 >> [ 65%] Built target md >> make[1]: Leaving directory >> `/home/ffavela/Downloads/gromacs-4.6/build-cmake' >> make: *** [all] Error 2 >> > > This isn't the error message. It is further up. Please post it. > > >> NOTE: after an eventual successful installation, where can I find >> information of how to get the benefits of gromacs-gpu? -- >> > see > http://www.gromacs.org/Documentation/Cut-off_schemes > http://www.gromacs.org/Documentation/Performance_checklist > > Roland > > >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http
Re: [gmx-users] grimaces 4.6 installation error
On Thu, Jan 31, 2013 at 8:18 PM, Fernando Favela wrote: > Dear Gromacs users, > > I'm trying to install GMX 4.6 in a 64 Bit Machine with Nvidia GTX 680 > cards, I've already installed the intel compilers, cuda 5 and openmpi. > > I do the following procedure: > CC=/opt/intel/bin/icc CXX=/opt/intel/bin/icpc cmake .. > > then > > sudo make -j 12 > > and I get this error: > > Linking CXX shared library libmd.so > cd /home/ffavela/Downloads/gromacs-4.6/build-cmake/src/mdlib && > /usr/bin/cmake -E cmake_link_script CMakeFiles/md.dir/link.txt --verbose=1 > /opt/intel/bin/icpc -fPIC -mavx -Wall -ip -funroll-all-loops -O3 -DNDEBUG > -shared -Wl,-soname,libmd.so.6 -o libmd.so.6 > CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_gpu_ref.c.o > CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_simd_4xn.c.o > CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_common.c.o > CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_simd_2xnn.c.o > CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_ref.c.o > CMakeFiles/md.dir/genborn_allvsall.c.o CMakeFiles/md.dir/qm_mopac.c.o > CMakeFiles/md.dir/mvxvf.c.o CMakeFiles/md.dir/genborn.c.o > CMakeFiles/md.dir/ebin.c.o CMakeFiles/md.dir/csettle.c.o > CMakeFiles/md.dir/genborn_allvsall_sse2_single.c.o > CMakeFiles/md.dir/pme.c.o CMakeFiles/md.dir/gmx_fft.c.o > CMakeFiles/md.dir/force.c.o CMakeFiles/md.dir/qm_gaussian.c.o > CMakeFiles/md.dir/qm_orca.c.o CMakeFiles/md.dir/mdatom.c.o > CMakeFiles/md.dir/stat.c.o CMakeFiles/md.dir/perf_est.c.o > CMakeFiles/md.dir/domdec_network.c.o CMakeFiles/md.dir/pme_pp.c.o > CMakeFiles/md.dir/calcmu.c.o CMakeFiles/md.dir/shakef.c.o > CMakeFiles/md.dir/fft5d.c.o CMakeFiles/md.dir/tables.c.o > CMakeFiles/md.dir/qmmm.c.o CMakeFiles/md.dir/domdec_con.c.o > CMakeFiles/md.dir/clincs.c.o CMakeFiles/md.dir/domdec_setup.c.o > CMakeFiles/md.dir/gmx_wallcycle.c.o CMakeFiles/md.dir/gmx_fft_fftw3.c.o > CMakeFiles/md.dir/partdec.c.o CMakeFiles/md.dir/domdec.c.o > CMakeFiles/md.dir/genborn_allvsall_sse2_double.c.o > CMakeFiles/md.dir/md_support.c.o CMakeFiles/md.dir/vsite.c.o > CMakeFiles/md.dir/groupcoord.c.o CMakeFiles/md.dir/mdebin.c.o > CMakeFiles/md.dir/gmx_fft_fftpack.c.o CMakeFiles/md.dir/tgroup.c.o > CMakeFiles/md.dir/vcm.c.o CMakeFiles/md.dir/nsgrid.c.o > CMakeFiles/md.dir/nbnxn_search.c.o CMakeFiles/md.dir/constr.c.o > CMakeFiles/md.dir/shellfc.c.o CMakeFiles/md.dir/iteratedconstraints.c.o > CMakeFiles/md.dir/rf_util.c.o CMakeFiles/md.dir/update.c.o > CMakeFiles/md.dir/genborn_sse2_double.c.o CMakeFiles/md.dir/forcerec.c.o > CMakeFiles/md.dir/nbnxn_atomdata.c.o > CMakeFiles/md.dir/genborn_sse2_single.c.o CMakeFiles/md.dir/gmx_fft_mkl.c.o > CMakeFiles/md.dir/pull.c.o CMakeFiles/md.dir/domdec_box.c.o > CMakeFiles/md.dir/domdec_top.c.o CMakeFiles/md.dir/mdebin_bar.c.o > CMakeFiles/md.dir/nlistheuristics.c.o CMakeFiles/md.dir/qm_gamess.c.o > CMakeFiles/md.dir/coupling.c.o CMakeFiles/md.dir/adress.c.o > CMakeFiles/md.dir/init.c.o CMakeFiles/md.dir/wnblist.c.o > CMakeFiles/md.dir/expanded.c.o CMakeFiles/md.dir/wall.c.o > CMakeFiles/md.dir/ns.c.o CMakeFiles/md.dir/minimize.c.o > CMakeFiles/md.dir/sim_util.c.o CMakeFiles/md.dir/pullutil.c.o > CMakeFiles/md.dir/gmx_parallel_3dfft.c.o CMakeFiles/md.dir/edsam.c.o > CMakeFiles/md.dir/pull_rotation.c.o CMakeFiles/md.dir/gmx_fft_acml.c.o > CMakeFiles/md.dir/tpi.c.o CMakeFiles/md.dir/ewald.c.o > CMakeFiles/md.dir/calcvir.c.o nbnxn_cuda/libnbnxn_cuda.a > ../gmxlib/libgmx.so.6 /usr/lib/libblas.so.3gf /usr/lib/liblapack.so.3gf > /usr/lib/libblas.so.3gf -ldl -lm -lfftw3f -openmp /usr/lib/liblapack.so.3gf > -ldl -lm -lfftw3f ../gmxlib/gpu_utils/libgpu_utils.a > ../gmxlib/cuda_tools/libcuda_tools.a /usr/local/cuda/lib64/libcudart.so > -lcuda -lpthread > -Wl,-rpath,/home/ffavela/Downloads/gromacs-4.6/build-cmake/src/gmxlib:/usr/local/cuda/lib64: > cd /home/ffavela/Downloads/gromacs-4.6/build-cmake/src/mdlib && > /usr/bin/cmake -E cmake_symlink_library libmd.so.6 libmd.so.6 libmd.so > make[2]: Leaving directory > `/home/ffavela/Downloads/gromacs-4.6/build-cmake' > /usr/bin/cmake -E cmake_progress_report > /home/ffavela/Downloads/gromacs-4.6/build-cmake/CMakeFiles 89 90 91 92 93 > 94 95 96 97 > [ 65%] Built target md > make[1]: Leaving directory > `/home/ffavela/Downloads/gromacs-4.6/build-cmake' > make: *** [all] Error 2 > This isn't the error message. It is further up. Please post it. > NOTE: after an eventual successful installation, where can I find > information of how to get the benefits of gromacs-gpu? -- > see http://www.gromacs.org/Documentation/Cut-off_schemes http://www.gromacs.org/Documentation/Performance_checklist 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
[gmx-users] grimaces 4.6 installation error
Dear Gromacs users, I'm trying to install GMX 4.6 in a 64 Bit Machine with Nvidia GTX 680 cards, I've already installed the intel compilers, cuda 5 and openmpi. I do the following procedure: CC=/opt/intel/bin/icc CXX=/opt/intel/bin/icpc cmake .. then sudo make -j 12 and I get this error: Linking CXX shared library libmd.so cd /home/ffavela/Downloads/gromacs-4.6/build-cmake/src/mdlib && /usr/bin/cmake -E cmake_link_script CMakeFiles/md.dir/link.txt --verbose=1 /opt/intel/bin/icpc -fPIC -mavx -Wall -ip -funroll-all-loops -O3 -DNDEBUG -shared -Wl,-soname,libmd.so.6 -o libmd.so.6 CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_gpu_ref.c.o CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_simd_4xn.c.o CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_common.c.o CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_simd_2xnn.c.o CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_ref.c.o CMakeFiles/md.dir/genborn_allvsall.c.o CMakeFiles/md.dir/qm_mopac.c.o CMakeFiles/md.dir/mvxvf.c.o CMakeFiles/md.dir/genborn.c.o CMakeFiles/md.dir/ebin.c.o CMakeFiles/md.dir/csettle.c.o CMakeFiles/md.dir/genborn_allvsall_sse2_single.c.o CMakeFiles/md.dir/pme.c.o CMakeFiles/md.dir/gmx_fft.c.o CMakeFiles/md.dir/force.c.o CMakeFiles/md.dir/qm_gaussian.c.o CMakeFiles/md.dir/qm_orca.c.o CMakeFiles/md.dir/mdatom.c.o CMakeFiles/md.dir/stat.c.o CMakeFiles/md.dir/perf_est.c.o CMakeFiles/md.dir/domdec_network.c.o CMakeFiles/md.dir/pme_pp.c.o CMakeFiles/md.dir/calcmu.c.o CMakeFiles/md.dir/shakef.c.o CMakeFiles/md.dir/fft5d.c.o CMakeFiles/md.dir/tables.c.o CMakeFiles/md.dir/qmmm.c.o CMakeFiles/md.dir/domdec_con.c.o CMakeFiles/md.dir/clincs.c.o CMakeFiles/md.dir/domdec_setup.c.o CMakeFiles/md.dir/gmx_wallcycle.c.o CMakeFiles/md.dir/gmx_fft_fftw3.c.o CMakeFiles/md.dir/partdec.c.o CMakeFiles/md.dir/domdec.c.o CMakeFiles/md.dir/genborn_allvsall_sse2_double.c.o CMakeFiles/md.dir/md_support.c.o CMakeFiles/md.dir/vsite.c.o CMakeFiles/md.dir/groupcoord.c.o CMakeFiles/md.dir/mdebin.c.o CMakeFiles/md.dir/gmx_fft_fftpack.c.o CMakeFiles/md.dir/tgroup.c.o CMakeFiles/md.dir/vcm.c.o CMakeFiles/md.dir/nsgrid.c.o CMakeFiles/md.dir/nbnxn_search.c.o CMakeFiles/md.dir/constr.c.o CMakeFiles/md.dir/shellfc.c.o CMakeFiles/md.dir/iteratedconstraints.c.o CMakeFiles/md.dir/rf_util.c.o CMakeFiles/md.dir/update.c.o CMakeFiles/md.dir/genborn_sse2_double.c.o CMakeFiles/md.dir/forcerec.c.o CMakeFiles/md.dir/nbnxn_atomdata.c.o CMakeFiles/md.dir/genborn_sse2_single.c.o CMakeFiles/md.dir/gmx_fft_mkl.c.o CMakeFiles/md.dir/pull.c.o CMakeFiles/md.dir/domdec_box.c.o CMakeFiles/md.dir/domdec_top.c.o CMakeFiles/md.dir/mdebin_bar.c.o CMakeFiles/md.dir/nlistheuristics.c.o CMakeFiles/md.dir/qm_gamess.c.o CMakeFiles/md.dir/coupling.c.o CMakeFiles/md.dir/adress.c.o CMakeFiles/md.dir/init.c.o CMakeFiles/md.dir/wnblist.c.o CMakeFiles/md.dir/expanded.c.o CMakeFiles/md.dir/wall.c.o CMakeFiles/md.dir/ns.c.o CMakeFiles/md.dir/minimize.c.o CMakeFiles/md.dir/sim_util.c.o CMakeFiles/md.dir/pullutil.c.o CMakeFiles/md.dir/gmx_parallel_3dfft.c.o CMakeFiles/md.dir/edsam.c.o CMakeFiles/md.dir/pull_rotation.c.o CMakeFiles/md.dir/gmx_fft_acml.c.o CMakeFiles/md.dir/tpi.c.o CMakeFiles/md.dir/ewald.c.o CMakeFiles/md.dir/calcvir.c.o nbnxn_cuda/libnbnxn_cuda.a ../gmxlib/libgmx.so.6 /usr/lib/libblas.so.3gf /usr/lib/liblapack.so.3gf /usr/lib/libblas.so.3gf -ldl -lm -lfftw3f -openmp /usr/lib/liblapack.so.3gf -ldl -lm -lfftw3f ../gmxlib/gpu_utils/libgpu_utils.a ../gmxlib/cuda_tools/libcuda_tools.a /usr/local/cuda/lib64/libcudart.so -lcuda -lpthread -Wl,-rpath,/home/ffavela/Downloads/gromacs-4.6/build-cmake/src/gmxlib:/usr/local/cuda/lib64: cd /home/ffavela/Downloads/gromacs-4.6/build-cmake/src/mdlib && /usr/bin/cmake -E cmake_symlink_library libmd.so.6 libmd.so.6 libmd.so make[2]: Leaving directory `/home/ffavela/Downloads/gromacs-4.6/build-cmake' /usr/bin/cmake -E cmake_progress_report /home/ffavela/Downloads/gromacs-4.6/build-cmake/CMakeFiles 89 90 91 92 93 94 95 96 97 [ 65%] Built target md make[1]: Leaving directory `/home/ffavela/Downloads/gromacs-4.6/build-cmake' make: *** [all] Error 2 I think this issue must be related with the compilers because if I use the default gnu compilers the problem disappear. Could anybody help me please? Thanks in advance. Fernando. NOTE: after an eventual successful installation, where can I find information of how to get the benefits of gromacs-gpu? -- 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: Re: Inquiry about a completely user defined force field
On 1/31/13 6:17 PM, S. Alireza Bagherzadeh wrote: -- Message: 1 Date: Thu, 31 Jan 2013 16:57:56 -0500 From: Justin Lemkul Subject: Re: [gmx-users] Re: Inquiry about a completely user defined force field To: Discussion list for GROMACS users Message-ID: <510ae8e4.10...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 1/31/13 1:57 PM, S. Alireza Bagherzadeh wrote: Dear Dr.Abraham, Thank you for taking the time to look at my files. However, I have one question remained in my mind: Where is the "atomtypes.atp" used in the force field? I suspect that this file is only for clarification for the user in order to eliminate/minimize confusion and this file is not read by the program. Am I correct? No, the .atp file is used by pdb2gmx. See the manual. Dear Justin, I am not using pdb2gmx in any steps of preparation of my input files. I have written a short script myself that converts my .xyz files to .gro files. So, this (not using the "atomtypes.atp" file) should not be a problem for me... Nor would I expect it. But since you asked... ;) I would also like to ask you for any insight on why in my system the tempera ture keeps increasing linearly with time under NVE ensemble (even up to unrealistic T of 550K)? I have verified this force filed with DL_POLY and my system showed a gradual temperature decrease which is the correct physical behavior of the system. Sorry, can't comment here. Without an .mdp file, it's hard to say anything. Apologies if you posted it before and I missed it. Here is my .mdp file. I appreciate it if you could take a look and point out any possible errors to me: General points: http://www.gromacs.org/Documentation/Terminology/NVE Specific comments below. ;- ; ;-; ; Run control integrator = md ; Leap-frog algorithm tinit= 0; starting time [ps] dt = 0.001; time step [ps] nsteps = 100 ; number of steps nstcomm = 100 ; frequency for center of mass motion removal [steps] ;-; ;-; ; Output control nstxout = 1000; frequency to write coordinates to output trajectory file [steps] nstvout = 0; frequency to write velocities to output trajectory file [steps] nstfout = 0; frequency to write forces to output trajectory file [steps] nstlog = 500 ; frequency to write energies to log file [steps] nstenergy= 500 ; frequency to write energies to energy file [steps] nstxtcout= 1000 ; frequency to write coordinates to xtc trajectory [steps] xtc-precision= 1000 ; precision to write to xtc trajectory [real] xtc_grps = HYDW HYDG SOL energygrps = HYDW HYDG SOL SiO2 SiOH ;-; ;-; ; Neighborsearching and short-range nonbonded interactions nstlist = 10 ; frequency to update the neighbor list nstlist may be fine, consider using -1 as suggested by the link above. [steps] ns_type = grid ; (grid / simple) search for neighboring list pbc = xyz ; priodic boundary conditions (xyz / no / xy) rlist= 1.0 ; cut-off distance for the short-range Again, per the link above, rlist should be larger than max(rcoulomb,rvdw) so you may need to increase this value. neighbor list [nm] ;-; ;-; ; Electrostatics coulombtype = PME rcoulomb = 1.0 ; distance for the Coulomb cut-off [nm] ;-; ;-; ; van der Waals vdw-type = switch ; (the LJ normal out at rvdw_switch to reach zero at rvdw) rvdw-switch = 0.8 ; where to strat switching the LJ potential [nm] rvdw = 0.9 ; cut-off distance for vdw potenrial [nm] DispCorr
Re: [gmx-users] g_x2top is missing bonds
On 1/31/13 5:09 PM, FX wrote: It would be useful to see the .n2t file and the screen output about what's problematic. g_x2top cannot identify suitable entries in the .n2t file for 36 of your atoms, so some combination of atoms is not accounted for, either by omission in the .n2t file or from a configuration that doesn't allow for combinations to be matched. I uploaded the files here: https://www.dropbox.com/s/w4ubappzljmkw35/gromacs.zip The thing is: if I take the example of ZN atoms, they are all equivalent by symmetry operations, so there's really only one type, and some of the ZN atoms are found by g_x2top. Things I have thought of so far: -- It could possibly be some rounding issue, but I seems that the source code of g_x2top uses a 10% tolerance, which is more than enough for my system. -- PBC issue? But some of the atoms near the cell boundaries are fine Some are fine, others are way off. The first two atoms g_x2top complains about are C3 and C5. Turning on a periodic reference shows that C3 (missing two bonds) is 0.077 and 0.197 nm away from the two N atoms to which it should be bonded, far from the specified value of 0.130. C5 (missing one bond) is similar, because one of the N atoms is 0.221 nm away, while the other N is fine at 0.126 nm. I didn't check the rest, but I suspect the same issues apply. -Justin Attachments to the list are not accepted due to problems in the past. It's best to post a link from which any necessary files can be downloaded. Occasionally snippets of files are appropriate, but often times omitted information can be important and you might not know it ;) Being involved in other open-source projects, I see very well what you mean. Thanks for your time, FX-- 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 -- 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] g_x2top is missing bonds
> try acpype iso g_x2top (this comes straight from the developer). Two questions: 1. How's that supposed to work? I tried, it doesn't work, acpype does not know "iso" or "g_x2top" arguments 2. I'm not using AMBER as forcefield, so I'm not sure if that wrapper on ambertools is appropriate Thanks, FX-- 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_x2top is missing bonds
> It would be useful to see the .n2t file and the screen output about what's > problematic. g_x2top cannot identify suitable entries in the .n2t file for > 36 of your atoms, so some combination of atoms is not accounted for, either > by omission in the .n2t file or from a configuration that doesn't allow for > combinations to be matched. I uploaded the files here: https://www.dropbox.com/s/w4ubappzljmkw35/gromacs.zip The thing is: if I take the example of ZN atoms, they are all equivalent by symmetry operations, so there's really only one type, and some of the ZN atoms are found by g_x2top. Things I have thought of so far: -- It could possibly be some rounding issue, but I seems that the source code of g_x2top uses a 10% tolerance, which is more than enough for my system. -- PBC issue? But some of the atoms near the cell boundaries are fine > Attachments to the list are not accepted due to problems in the past. It's > best to post a link from which any necessary files can be downloaded. > Occasionally snippets of files are appropriate, but often times omitted > information can be important and you might not know it ;) Being involved in other open-source projects, I see very well what you mean. Thanks for your time, FX-- 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_x2top is missing bonds
On 2013-01-31 22:55, FX wrote: Hey Matt, (It's a small world, eh?) I don't have a particular reason to use Gromacs. I used it for small ions solvation ten years back, I liked it, but every time I have tried to use it since for crystalline systems, I was put off because, as you say, it's probably not what it's designed for. In that particular case, I set out to use Gromacs because I'm working to reproduce a published paper that used Gromacs. Anyway, I'm interested in this new thread development (and suggestions as to alternatives more suited to my system), but also in suggestions regarding my original question :) Cheers, FX-- 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 try acpype iso g_x2top (this comes straight from the developer). -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Removal of global rotation/translation
On 1/31/13 11:53 AM, George Patargias wrote: Dear Gromacs list I would like to ask a question regarding the global rotation and translation removal in GROMACS. In my mdp file I use the following options: ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 10 ; group(s) for center of mass motion removal comm-grps= Are these options ensuring that global rotation and translation is removed every 10 steps? More directly, it removes net motion of the center of mass, thus avoiding problems like the flying ice cube. Is the trjconv command (as issued below) also removing global rotation and translation? trjconv -f traj_Total.xtc -s prod1.tpr -o rot+trans.xtc -fit rot+trans Not necessarily global motions, but you can apply the fitting to whatever subset of atoms you like. In which case is the "-center" option in trjconv is used? Many. trjconv is sort of a Swiss army knife, capable of doing dozens of things if the right options are applied. The -center option is probably most often used to center a simple solute in the box in every frame. -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: Inquiry about a completely user defined force field
On 1/31/13 1:57 PM, S. Alireza Bagherzadeh wrote:
Dear Dr.Abraham,
Thank you for taking the time to look at my files.
However, I have one question remained in my mind:
Where is the "atomtypes.atp" used in the force field?
I suspect that this file is only for clarification for the user in
order to eliminate/minimize
confusion and this file is not read by the program. Am I correct?
No, the .atp file is used by pdb2gmx. See the manual.
I would also like to ask you for any insight on why in my system the tempera
ture keeps increasing linearly with time under NVE ensemble (even up to
unrealistic T of 550K)? I have verified this force filed with DL_POLY and
my system showed a gradual temperature decrease which is the correct
physical behavior of the system.
Sorry, can't comment here. Without an .mdp file, it's hard to say anything.
Apologies if you posted it before and I missed it.
One clue which might be useful is that even though when I hand-calculate
the total charge of my system to be zero, the gormacs warns me that my
system has the total charge of 0.000108. Could this be the reason? Do you
have any suggestions for me to solve this potential problem? (I am not
using gromacs in double-precision mode).
Probably just a normal consequence of floating-point math. Check the topology
to be sure.
http://www.gromacs.org/Documentation/Errors#System_has_non-zero_total_charge
-Justin
Best regards,
Alireza
Today's Topics:
1. Protein in vacum (Shima Arasteh)
2. Re: Inquiry about a completely user defined force field
(Mark Abraham)
--
Message: 2
Date: Mon, 28 Jan 2013 11:59:37 +0100
From: Mark Abraham
Subject: Re: [gmx-users] Inquiry about a completely user defined force
field
To: Discussion list for GROMACS users
Message-ID:
<
camnumarsfd+wrwqrcpujipsvczypz8kujvaxd9h4ko51zlb...@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
There's nothing that leaps out at me as being wrong - but syntax checking
is the job of the parser (grompp) and logic checking can only be done by
you. To do that, I would proceed slowly, demonstrating that small chunks of
the force field can be used to generate results you can validate against
something external (e.g. experiment, or a reference implementation of the
force field). Don't just grab your simulation system and assume everything
works!
Mark
On Mon, Jan 28, 2013 at 7:35 AM, S. Alireza Bagherzadeh <
s.a.bagherzade...@gmail.com> wrote:
Dear gmx-users,
I am simulating a system in which I have a force field that is not
included
in gromacs forcefields.
So, I decided to construct my own force field in a sub-directory of my
actual
run.
I read chapter 5 of gromacs 4.5.4 user manual (pgs. 107-139) and I
prepared
the following files.
Below I am copying the content of a few sample files as well as my
topology
file.
I appreciate it if you could take a look and advise me whether anything
is
missing, wrong or incomplete.
Best regards,
*{topol.top}:*
; Topology for methane hydrate between silica surfaces in contact with
water and gas
#include
"/home/alireza/Silica_H2O_Gas_Hyd_Decomp/topol_preparation/myff.ff/forcefield.itp"
;Hydrate
;---
; water topology - hydrate phase
#include
"/home/alireza/Silica_H2O_Gas_Hyd_Decomp/topol_preparation/myff.ff/spce_hyd.itp"
; methane topology - large cages of hydrate phase
#include
"/home/alireza/Silica_H2O_Gas_Hyd_Decomp/topol_preparation/myff.ff/UAmethane_lc.itp"
; methane topology - small cages of hydrate phase
#include
"/home/alireza/Silica_H2O_Gas_Hyd_Decomp/topol_preparation/myff.ff/UAmethane_sc.itp"
;
; water topology - liquid water
#include
"/home/alireza/Silica_H2O_Gas_Hyd_Decomp/topol_preparation/myff.ff/spce_liq.itp"
;Silica
;
; silica topology - bulk Si
#include
"/home/alireza/Silica_H2O_Gas_Hyd_Decomp/topol_preparation/myff.ff/SilicaLopez_Si.itp"
; silica topology - bulk O
#include
"/home/alireza/Silica_H2O_Gas_Hyd_Decomp/topol_preparation/myff.ff/SilicaLopez_Oi.itp"
; silica topology - surface O
#include
"/home/alireza/Silica_H2O_Gas_Hyd_Decomp/topol_preparation/myff.ff/SilicaLopez_Os.itp"
; silica topology - surface H
#include
"/home/alireza/Silica_H2O_Gas_Hyd_Decomp/topol_preparation/myff.ff/SilicaLopez_Hs.itp"
;-
[ system ]
; Name
Methane hydrate between 2 silica surfaces in contact with water and gas
[ molecules ]
; Compound #mols
HydrateW 2322
HydG_sc81
HydG_lc276
SOL3413
Silica_Si 1848
Silica_Oi 3360
Silica_Os 672
Silica_Hs 672
*SAMPLE FORCE FIELD FILES:*
*{atomtypes.atp}:*
;atmnm mass
Description
Reference
O 15.99940 ; water oxygen (hydrate & liquid phase),
tip4p-ice
Re: [gmx-users] g_x2top is missing bonds
Hey Matt, (It's a small world, eh?) I don't have a particular reason to use Gromacs. I used it for small ions solvation ten years back, I liked it, but every time I have tried to use it since for crystalline systems, I was put off because, as you say, it's probably not what it's designed for. In that particular case, I set out to use Gromacs because I'm working to reproduce a published paper that used Gromacs. Anyway, I'm interested in this new thread development (and suggestions as to alternatives more suited to my system), but also in suggestions regarding my original question :) Cheers, FX-- 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_x2top is missing bonds
On 1/31/13 4:10 PM, Matt Watkins wrote: Oops. Well, I'd be interested in people's opinions and don't intend to hijack FX's thread. I do use the code regularly and greatly appreciate all the effort that people have put into its development. But, particularly, the inability to easily mix buckingham and lennard-jones is awkward for easily mixing inorganic/organic systems. Apologies again to those offended, and maybe it could be a useful discussion, Feature requests are always welcome on redmine.gromacs.org. In the past 7 or so years of reading this list, I can count on one hand the amount of times people have asked about mixing Buckingham and LJ interactions, if that gives you any idea. Either people who want it are very quiet, or there's not a very persistent need for such features. The core development team only implements what they feel is generally useful or has been necessary for their own work. There is only so much time to get all these things done, and version 4.6 IMHO represents a heroic amount of effort given all the new toys we have to play with. If people have useful contributions for various features, they are always welcome. Gromacs is open-source for a reason :) Gromacs was indeed built around biomolecular simulations, but I have seen people do rather elegant and creative work with other systems. Any time I do anything particularly crafty, I write a tutorial ;) Gromacs is very user-driven. We are on our way to version 5.0, which will likely represent significant change to just about everything. If there are features you want (or even better, are willing to help develop), Redmine is the place to file away wishlists, and the gmx-developers mailing list is the appropriate forum to talk about code. -Justin On Thu, 31 Jan 2013 19:32:36 -, FX wrote: Hello, I'm trying to prepare a MD of a hybrid organic-inorganic crystal, i.e. only one big molecule extending throughout space with PBC. I have prepared my .gro file from the PDB (and checked it with babel/vmd). I'm trying to generate the topology with g_x2top. I have: - created a directory for my forcefield - suitable atomname2type.n2t in there - forcefield.itp file with my bonded forcefield parameters However, g_x2top complains about not finding the expected number of bonds: g_x2top -f zif8.gro -o topol.top -ff myff -name test -pbc Fatal error: Could only find a forcefield type for 240 out of 276 atoms The weird part is: all zinc atoms should be equivalent, so there is no reason for some to have 2 or 3 bonds while the others have 4 (as expected). Given that the .gro file is correct (including PBC), where could the problem come from? And how to diagnose it further? Thanks in advance for any hint, and apologies if I've not given enough information (or too much). Sincerely, FX PS: I don't know what's the policy on this list, so in doubt I attach the directory with my files -- 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 -- 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] g_x2top is missing bonds
On 1/31/13 2:32 PM, FX wrote: Hello, I'm trying to prepare a MD of a hybrid organic-inorganic crystal, i.e. only one big molecule extending throughout space with PBC. I have prepared my .gro file from the PDB (and checked it with babel/vmd). I'm trying to generate the topology with g_x2top. I have: - created a directory for my forcefield - suitable atomname2type.n2t in there - forcefield.itp file with my bonded forcefield parameters However, g_x2top complains about not finding the expected number of bonds: g_x2top -f zif8.gro -o topol.top -ff myff -name test -pbc Fatal error: Could only find a forcefield type for 240 out of 276 atoms The weird part is: all zinc atoms should be equivalent, so there is no reason for some to have 2 or 3 bonds while the others have 4 (as expected). Given that the .gro file is correct (including PBC), where could the problem come from? And how to diagnose it further? Thanks in advance for any hint, and apologies if I've not given enough information (or too much). It would be useful to see the .n2t file and the screen output about what's problematic. g_x2top cannot identify suitable entries in the .n2t file for 36 of your atoms, so some combination of atoms is not accounted for, either by omission in the .n2t file or from a configuration that doesn't allow for combinations to be matched. Sincerely, FX PS: I don't know what's the policy on this list, so in doubt I attach the directory with my files Attachments to the list are not accepted due to problems in the past. It's best to post a link from which any necessary files can be downloaded. Occasionally snippets of files are appropriate, but often times omitted information can be important and you might not know it ;) -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] g_x2top is missing bonds
Oops. Well, I'd be interested in people's opinions and don't intend to hijack FX's thread. I do use the code regularly and greatly appreciate all the effort that people have put into its development. But, particularly, the inability to easily mix buckingham and lennard-jones is awkward for easily mixing inorganic/organic systems. Apologies again to those offended, and maybe it could be a useful discussion, Matt On Thu, 31 Jan 2013 19:32:36 -, FX wrote: Hello, I'm trying to prepare a MD of a hybrid organic-inorganic crystal, i.e. only one big molecule extending throughout space with PBC. I have prepared my .gro file from the PDB (and checked it with babel/vmd). I'm trying to generate the topology with g_x2top. I have: - created a directory for my forcefield - suitable atomname2type.n2t in there - forcefield.itp file with my bonded forcefield parameters However, g_x2top complains about not finding the expected number of bonds: g_x2top -f zif8.gro -o topol.top -ff myff -name test -pbc Fatal error: Could only find a forcefield type for 240 out of 276 atoms The weird part is: all zinc atoms should be equivalent, so there is no reason for some to have 2 or 3 bonds while the others have 4 (as expected). Given that the .gro file is correct (including PBC), where could the problem come from? And how to diagnose it further? Thanks in advance for any hint, and apologies if I've not given enough information (or too much). Sincerely, FX PS: I don't know what's the policy on this list, so in doubt I attach the directory with my files -- 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 -- Dr Matthew Watkins Dept. of Physics and Astronomy University College London phone: +44 20 7679 3436 -- 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_x2top is missing bonds
Hey FX, out of interest (and I ask off list as it is probably not very politically correct) why do you want to use gromacs? I've found it to be a nightmare for other than proteins/trivial systems. Hope things are well, Matt On Thu, 31 Jan 2013 19:32:36 -, FX wrote: Hello, I'm trying to prepare a MD of a hybrid organic-inorganic crystal, i.e. only one big molecule extending throughout space with PBC. I have prepared my .gro file from the PDB (and checked it with babel/vmd). I'm trying to generate the topology with g_x2top. I have: - created a directory for my forcefield - suitable atomname2type.n2t in there - forcefield.itp file with my bonded forcefield parameters However, g_x2top complains about not finding the expected number of bonds: g_x2top -f zif8.gro -o topol.top -ff myff -name test -pbc Fatal error: Could only find a forcefield type for 240 out of 276 atoms The weird part is: all zinc atoms should be equivalent, so there is no reason for some to have 2 or 3 bonds while the others have 4 (as expected). Given that the .gro file is correct (including PBC), where could the problem come from? And how to diagnose it further? Thanks in advance for any hint, and apologies if I've not given enough information (or too much). Sincerely, FX PS: I don't know what's the policy on this list, so in doubt I attach the directory with my files -- 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 -- Dr Matthew Watkins Dept. of Physics and Astronomy University College London phone: +44 20 7679 3436 -- 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_x2top is missing bonds
Hello, I'm trying to prepare a MD of a hybrid organic-inorganic crystal, i.e. only one big molecule extending throughout space with PBC. I have prepared my .gro file from the PDB (and checked it with babel/vmd). I'm trying to generate the topology with g_x2top. I have: - created a directory for my forcefield - suitable atomname2type.n2t in there - forcefield.itp file with my bonded forcefield parameters However, g_x2top complains about not finding the expected number of bonds: > g_x2top -f zif8.gro -o topol.top -ff myff -name test -pbc > Fatal error: > Could only find a forcefield type for 240 out of 276 atoms The weird part is: all zinc atoms should be equivalent, so there is no reason for some to have 2 or 3 bonds while the others have 4 (as expected). Given that the .gro file is correct (including PBC), where could the problem come from? And how to diagnose it further? Thanks in advance for any hint, and apologies if I've not given enough information (or too much). Sincerely, FX PS: I don't know what's the policy on this list, so in doubt I attach the directory with my files -- 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] choice of the hydrogen name added thanks to .hdb file ?
Hello, I would like to know if it's possible to give a specific name to an hydrogen which will be added thanks to the .hdb file. Indeed, by default, the hydrogens added on the same carbon have the same name with the last number incremented by 1. Example : for charmm36, the hydrogens added to the CB atom of ARG are named HB1 & HB2 thanks to the line "2 6 HB CB CG CA" in the aminoacids.hdb file. But if I want the names H1A & H1B ? If i write the lines "2 6 H1 CB CG CA" in the aminoacids.hdb file, the hydrogens will have the names H11 & H12. I ask this question because I would like to add hydrogens to lipids automatically and the difference between hydrogens on the same atom depends of a letter and not a number in charmm36. (H13A, H13B H13C are linked to C13 in POPC for example) Thank you. -- View this message in context: http://gromacs.5086.n6.nabble.com/choice-of-the-hydrogen-name-added-thanks-to-hdb-file-tp5005051.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] Removal of global rotation/translation
Dear Gromacs list I would like to ask a question regarding the global rotation and translation removal in GROMACS. In my mdp file I use the following options: ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 10 ; group(s) for center of mass motion removal comm-grps= Are these options ensuring that global rotation and translation is removed every 10 steps? Is the trjconv command (as issued below) also removing global rotation and translation? trjconv -f traj_Total.xtc -s prod1.tpr -o rot+trans.xtc -fit rot+trans In which case is the "-center" option in trjconv is used? Thanks. George -- 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] Error in BlueGene
On 2013-01-30 23:48, Ricardo Soares wrote: Hello, before submitting to Bluegene, I always test the system in my local 8 core cpu, and if it works, it will also work in Bluegene, as long as I balance the domain decomposition for the larger number of cores. If your system insists in exploding, even after energy minimization, you could try to decrease the integration timestep (dt) to something lower than 2 fs, maybe to 1fs or, in some cases even 0.5 fs. Did you tried that? And check the energies. Which term causes the crash? Cheers, Ricardo. On Wed, 30 Jan 2013 15:44:53 -0200, Cintia C. Vequi-Suplicy wrote Mark, Thank you for your answer. I did an energy minimization with the file em.mdp (below) and then I did a 40 ns simulation with the same md.mdp I send before. These two steps were done in my local cluster. After that I took the configuration for the simulation in the bluegene and I got these error. I notice that the step that the error occurs depends on the number of nodes I use. I am also including the end of the min.out file. I also tried others integrators for the energy minimization but I always get the same error. Thank you again, Cíntia --- em.mdp integrator = steep tinit= 0.0 dt = 0.002 nsteps = 500 nstcomm = 1 comm-grps= Other SOL nstxout = 100 nstvout = 100 nstfout = 0 nstlog = 100 nstenergy= 100 nstxtcout= 100 xtc_precision= 100 xtc-grps = energygrps = Other SOL nstlist = 5 ns_type = grid pbc = xyz rlist= 1.4 coulombtype = reaction-field rcoulomb = 1.4 epsilon_rf = 66 vdw_type = cut-off rvdw = 1.4 DispCorr = No constraints = none --- min.out ... Step= 5192, Dmax= 1.9e-11 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, atom= 22015 Step= 5193, Dmax= 9.5e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, atom= 22015 Step= 5194, Dmax= 4.7e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, atom= 22015 Step= 5195, Dmax= 2.4e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, atom= 22015 Step= 5196, Dmax= 2.8e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, atom= 22015 Step= 5197, Dmax= 1.4e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, atom= 22015 Step= 5198, Dmax= 1.7e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02, atom= 22015 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 5199 steps, but did not reach the requested Fmax < 10. Potential Energy = -1.79302464181879e+06 Maximum force = 6.65022934447791e+02 on atom 22015 Norm of force = 4.90065871184878e+00 gcq#0: Thanx for Using GROMACS - Have a Nice Day --- --- md.mdp file integrator = md tinit= 0.0 dt = 0.002 nsteps = 500 nstcomm = 5 comm-grps= Other SOL nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 1000 nstenergy= 1000 nstxtcout= 1000 xtc_precision= 1000 xtc-grps = energygrps = Other SOL nstlist = 5 ns_type = grid pbc = xyz rlist= 1.4 coulombtype = reaction-field rcoulomb = 1.4 epsilon_rf = 66 vdw_type = cut-off rvdw = 1.4 DispCorr = No tcoupl = v-rescale tc-grps = Other SOL tau_t= 0.4 0.4 ref_t= 296 296 Pcoupl = berendsen Pcoupltype = semiisotropic tau_p= 0.2 0.2 compressibility = 4.51e-5 4.51e-5 ref_p= 1.0 1.0 constraints = hbonds constraint_algorithm = lincs -- 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_Lis
Re: [gmx-users] ligand topology
On 1/31/13 9:51 AM, az kalsom wrote: hi i have docked the compund with protein and selected the best protein-ligand conformation for simulations, but when i generate the topolgy for ligand by Automated Topology Builder (ATB) and Repository , job is killed every tym. error message is 1) geometry was inappropriate; (2) the number of hydrogen atoms or the net charge was inappropriate... what should i do to remove this ? There's clearly something wrong with your input, but since (1) we don't know what it is, (2) we don't know what you're doing, and (3) this forum isn't about ATB, it's pretty hard to help. Refer to the FAQ (http://compbio.biosci.uq.edu.au/atb/index.py?tab=faq_tab) and seek help from whatever resources ATB provides. -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] gcpr tutorial
On 1/31/13 3:19 AM, Najmeh Fani wrote: Hello please help me I have a question in gpcr tutorial when I run energy minimization process for inflategro with this command: grompp -f EM.mdp -c system_inflated.gro -p topol.top -o EM.tpr -maxwarn 5 I seen an error : Fatal error: [ file strong_posre.itp, line 57 ]: Atom index (53) in position_restraints out of bounds (1-52). This probably means that you have inserted topology section "position_restraints" in a part belonging to a different molecule than you intended to. In that case move the "position_restraints" section to the right molecule http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds You've either #included a position restraint file in the wrong place, or you're specifying atoms in the position restraint file that don't correspond to the [moleculetype] you're trying to restrain. -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] gcpr tutorial
Hello please help me I have a question in gpcr tutorial when I run energy minimization process for inflategro with this command: grompp -f EM.mdp -c system_inflated.gro -p topol.top -o EM.tpr -maxwarn 5 I seen an error : Fatal error: [ file strong_posre.itp, line 57 ]: Atom index (53) in position_restraints out of bounds (1-52). This probably means that you have inserted topology section "position_restraints" in a part belonging to a different molecule than you intended to. In that case move the "position_restraints" section to the right molecule -- View this message in context: http://gromacs.5086.n6.nabble.com/gcpr-tutorial-tp5005039.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
