[gmx-users] Missing oxyz in vmx distance output

[Nash, Anthony]

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