Hi all, I¹m really hoping this is my own oversight. Using Gromacs 5.0.4 (can¹t upgrade, this is a distribution on a cluster) I can generate each of the output options (-oav -oall -oh -oallstat) apart from -oxyz when I run the command:
gmx_d distance -f NPT_0_40ns_compress.gro -s NPT_0_40ns_compress.tpr -n distance.ndx -select 'com of group "A_N" plus com of group "A_C"' -oxyz It reports the average distance (absolute distance as there is only one frame but I have also tried this with a .trr with the same result), however, the distxyz.xvg is missing, even if I explicitly define ³-oxyz distxyz.xvg². I have also switched around the values of -pbc and -rmpbc incase there was an undefined dependency somewhere. Some of the output: ‹‹‹‹‹‹‹‹‹‹‹ GROMACS: gmx distance, VERSION 5.0.4 (double precision) Executable: /usr/local/gromacs/bin/gmx_d Library dir: /usr/local/gromacs/share/gromacs/top Command line: gmx_d distance -f NPT_0_40ns_compress.trr -s NPT_0_40ns_compress.tpr -n distance.ndx -select 'com of group "A_N" plus com of group "A_C"' -oxyz test.xvg Reading file NPT_0_40ns_compress.tpr, VERSION 5.0.4 (double precision) Reading file NPT_0_40ns_compress.tpr, VERSION 5.0.4 (double precision) trn version: GMX_trn_file (double precision) Last frame 2000 time 40000.000 Analyzed 2001 frames, last time 40000.000 A_N: Number of samples: 2001 Average distance: 7.373 nm Standard deviation: 0.625 nm Thanks Anthony Dr Anthony Nash Department of Chemistry University College London -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
