Unknown command-line option -ten in gmx msd gromacs

User discussions
1

Hi all,
I try to calculate MSD for LI ion in polymer electrolyte using gmx msd. i want to calculate complete msd as describe in gromacs manual using gmx msd command with -ten option. But when i used thgis gets the following error.

Command line:
gmx msd -f md-peoli15.xtc -o msd2-li.xvg -n peoli15.ndx -ten -dt 10 -b 5 -trestart 5

Program: gmx msd, version 2022.3
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 271)
Function: void gmx::CommandLineParser::parse(int*, char**)

Error in user input:
Invalid command-line options
Unknown command-line option -ten

where i am doing wrong please guide?

2

Hi!

Unfortunately, the documentation is outdated, the option was removed in GROMACS 2022. Sorry for the confusion.

We are looking into either updating the docs or bringing the feature back, but, unfortunately, no timeline for it yet.

3

HI
Can you also let me know the reason of this error i got while calculation gmx msd
Command line:
gmx msd -mol -f md-peoli15.xtc -s md-peoli15.tpr -o msd1-li.xvg -n peoli15.ndx -b 5 -trestart 10

Available static index groups:
Group 0 “System” (9720 atoms)
Group 1 “Other” (9705 atoms)
Group 2 “HYD” (15 atoms)
Group 3 “ETY” (9450 atoms)
Group 4 “OXY” (15 atoms)
Group 5 “MOL” (225 atoms)
Group 6 “LI” (15 atoms)
Group 7 “Ion” (15 atoms)
Group 8 “O1” (1350 atoms)
Group 9 “LI” (15 atoms)
Group 10 “MOL” (225 atoms)
Specify any number of selections for option ‘sel’
(Selections to compute MSDs for from the reference):
(one per line, for status/groups, ‘help’ for help, Ctrl-D to end)

9
Selection ‘9’ parsed
Reading file md-peoli15.tpr, VERSION 2022.3 (single precision)
Reading file md-peoli15.tpr, VERSION 2022.3 (single precision)
Reading frame 20 time 15.000

Program: gmx msd, version 2022.3

Standard library logic error (bug):
(exception type: St12length_error)
vector::_M_default_append

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation

4

Could you please share your input files? (Google Drive is okay if they are too large to upload here).