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Bug #3284

gmx msd cannot output two xvg files as suggested by command line option

Added by Christian Blau about 2 months ago.

Status:
New
Priority:
Normal
Category:
analysis tools
Affected version - extra info:
Affected version:
Difficulty:
simple
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Description

#request to fix msd xvg output behaviour

When using -mol and -o in gmx msd simulatneously, only the xvg files related to the -mol option are output and not the file related to the -o option.
We should either warn about the clashing command line options, or enable output of both.

Here is the original related user mail


hi, when i am using the command
 gmx msd -f prd.xtc -n il.ndx -s out3.tpr -mol -o msd.xvg

after that choosing a group the following line is coming.
Select a group to calculate mean squared displacement for:
Group     0 (         System) has  5616 elements
Group     1 (          Other) has  5616 elements
Group     2 (             c2) has  2376 elements
Group     3 (           ntf2) has  3240 elements
Group     4 (              N) has   216 elements
Group     5 (              N) has   216 elements
Select a group: 3
Selected 3: 'ntf2'
Split group of 3240 atoms into 216 molecules
Reading frame    5000 time 20000.000   Killed

and i cant get the msd file any suggestion regarding this??

thank you

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