Re: [gmx-users] Re: frame
well, you basically just did it… 20ns is 20,000ps. so trjconv -dump 19532 -s xxx -f xxx -- Dipl. Phys. Johannes Wagner PhD Student, MBM Group Klaus Tschira Lab (KTL) Max Planck Partner Institut for Computational Biology (PICB) 320 YueYang Road 200031 Shanghai, China phone: +86-21-54920475 email: johan...@picb.ac.cn and Heidelberg Institut for Theoretical Studies HITS gGmbH Schloß-Wolfsbrunnenweg 35 69118 Heidelberg Germany phone: +49-6221-533254 fax: +49 6221 533298 email: johannes.wag...@h-its.org http://www.h-its.org _ Amtsgericht Mannheim / HRB 337446 Managing Directors: Dr. h.c. Klaus Tschira Prof. Dr.-Ing. Andreas Reuter On 03.06.2013, at 16:50, maggin wrote: > How to convert ur frames in a time (ps)? > > Thank you very much! > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/frame-and-pdb-tp5008727p5008735.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 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] gmx 4.6.2 segementation fault (core dump)
hi, thanks for the prompt replies ~/programs/gromacs-4.6.2/bin$ ./mdrun -version Program: ./mdrun Gromacs version:VERSION 4.6.2 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled GPU support:enabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: AVX_256 FFT library:fftw-3.3.2-sse2 Large file support: enabled RDTSCP usage: enabled Built on: Fri May 31 18:44:32 CEST 2013 Built by: xx...@-its.org [CMAKE] Build OS/arch: Linux 3.8.8-100.fc17.x86_64 x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Core(TM) i5-3550 CPU @ 3.30GHz Build CPU family: 6 Model: 58 Stepping: 9 Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/lib64/ccache/cc GNU cc (GCC) 4.7.2 20120921 (Red Hat 4.7.2-2) C compiler flags: -mavx-Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -march=core-avx-i -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG C++ compiler: /usr/lib64/ccache/c++ GNU c++ (GCC) 4.7.2 20120921 (Red Hat 4.7.2-2) C++ compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG CUDA compiler: nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2012 NVIDIA Corporation;Built on Fri_Sep_21_17:28:58_PDT_2012;Cuda compilation tools, release 5.0, V0.2.1221 CUDA driver:5.0 CUDA runtime: 5.0 ~/programs/gromacs-4.6.2/bin/mdrun -o gpu.log -s gpu.tpr -v Back Off! I just backed up md.log to ./#md.log.1# Reading file gpu.tpr, VERSION 4.6.2 (single precision) Using 1 MPI thread Using 4 OpenMP threads 1 GPU detected: #0: NVIDIA GeForce GT 640, compute cap.: 3.0, ECC: no, stat: compatible 1 GPU auto-selected for this run: #0 Back Off! I just backed up traj.xtc to ./#traj.xtc.1# Back Off! I just backed up ener.edr to ./#ener.edr.1# starting mdrun 'triazole' 10 steps,100.0 ps. Segmentation fault (core dumped) .log file: 1,1Anfang Using a Gaussian width (1/beta) of 0.320163 nm for Ewald Cut-off's: NS: 1.004 Coulomb: 1 LJ: 1 System total charge: 0.000 Generated table with 1002 data points for Ewald. Tabscale = 500 points/nm Generated table with 1002 data points for LJ6. Tabscale = 500 points/nm Generated table with 1002 data points for LJ12. Tabscale = 500 points/nm Generated table with 1002 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1002 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1002 data points for 1-4 LJ12. Tabscale = 500 points/nm Using CUDA 8x8 non-bonded kernels Potential shift: LJ r^-12: 1.000 r^-6 1.000, Ewald 1.000e-05 Initialized non-bonded Ewald correction tables, spacing: 6.52e-04 size: 1536 Removing pbc first time Pinning threads with an auto-selected logical core stride of 1 Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest PLEASE READ AND CITE THE FOLLOWING REFERENCE G. Bussi, D. Donadio and M. Parrinello Canonical sampling through velocity rescaling J. Chem. Phys. 126 (2007) pp. 014101 --- Thank You --- There are: 18206 Atoms Initial temperature: 299.372 K Started mdrun on node 0 Mon Jun 3 16:09:59 2013 Step Time Lambda 00.00.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 2.04376e+042.58927e+049.76653e+001.50764e+02 -5.89359e+02 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential -2.69867e+05 -3.86496e+04 -4.94959e+043.97160e+03 -3.08139e+05 Kinetic En. Total EnergyTemperature Pressure (bar) 6.80836e+04 -2.40055e+052.99864e+02 -1.42021e+02 thats basically it. not much information, hence my email here in this list… cheers, Johannes -- Dipl. Phys. Johannes Wagner PhD Student, MBM Group Klaus Tschira Lab (KTL) Max Planck Partner Institut for Computational Biology (PICB) 320 YueYang Road 200031 Shanghai, China phone: +86-21-54920475 email: johan...@picb.ac.cn and Heidelberg Institut for Theoretical Studies HITS gGmbH Schloß-Wolfsbrunnenweg 35 69118 Heidelberg Germany phone: +49-6221-533254 fax: +49 6221 533298 email: johannes.wag...@h-its.org http://www.h-its.org _ Amtsgericht Mannheim / HRB 337446 Managing Directors:
Re: [gmx-users] frame
better to convert ur frames in a time (ps) and use trjconv -dump to write out the frame. -- Dipl. Phys. Johannes Wagner PhD Student, MBM Group Klaus Tschira Lab (KTL) Max Planck Partner Institut for Computational Biology (PICB) 320 YueYang Road 200031 Shanghai, China phone: +86-21-54920475 email: johan...@picb.ac.cn and Heidelberg Institut for Theoretical Studies HITS gGmbH Schloß-Wolfsbrunnenweg 35 69118 Heidelberg Germany phone: +49-6221-533254 fax: +49 6221 533298 email: johannes.wag...@h-its.org http://www.h-its.org _ Amtsgericht Mannheim / HRB 337446 Managing Directors: Dr. h.c. Klaus Tschira Prof. Dr.-Ing. Andreas Reuter On 03.06.2013, at 15:33, maggin wrote: > Hi, if I run 20ns MD, and want to get the pdb at 19532ps > > trjconv -s md_0_1.tpr -f md_0_1.xtc -o bovin19532.gro -dt 1 -b 19532 -e > 19532 > > editconf -f bovin19532.gro -o bovin19532.pdb > > If is it right? > > Thank you very much! > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/frame-tp5008727.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 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] gmx 4.6.2 segementation fault (core dump)
Hi there, trying to set up gmx-4.6.2, compiled with cuda 5.0.35 and gcc 4.7.2 on fedora linux, but it only gives me a "segementation fault (core dump)" on mdrun startup. Same compiling options on gmx 4.6.1 gives me a running mdrun. Did anyone encounter the same problem? Thanks, Johannes -- 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
