Change Default of --every Option of submit_gmx_analyses_lintf2_ether.py
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Change default of the --every option from 1 to 0. The value of the --every option is parsed to the -dt option of the submitted Gromacs tools. In the Gromacs documentation (https://manual.gromacs.org/documentation/2018-current/onlinehelp/gmx-trjconv.html) it says about the -dt option: > Only write/use frame when t MOD dt = first time (ps) However, when -dt is set to 1 and the spacing between frames is less than 1 ps, not every frame is processed, although t MOD 1 should be 0 for all (integer) values of t. When setting -dt 0, every frame is processed (although t MOD 0 should not be defined. However, 0 is the default value for -dt according to the docs).
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Change the default value of the `--every` option from 0 to 1. The value of the `--every` option is passed to the `-dt` option of the submitted Gromacs tools that support this option. The default value was set to 0 in PR #74 (#74), because `gmx trjconv` did not process all frames when `-dt` was set to 1 and the spacing between trajectory frames was less than 1 ps. However, it now turned out that the other Gromacs tools only process the first frame when `-dt` is set to 0. Therefore, we reset the default value for `--every` (i.e. `-dt`) to 1. In a following commit, we will replace the `-dt` option for `gmx trjconv` with `-skip`, which should be more robust (see https://www.mail-archive.com/gmx-users@gromacs.org/msg35903.html and https://www.mail-archive.com/gmx-users@gromacs.org/msg06868.html).
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Jun 22, 2023
…and `--dt`
Replace the `--every` option ("read every n-th frame from the
trajectory") by a `--skip` and `--dt` option. The new options mirror
the `-skip` and `-dt` options of Gromacs analysis tools and therefore
should by less confusing.
Related to pull request 119
(#119) and pull
request 74 (#74).
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Change Default of
--everyOption ofsubmit_gmx_analyses_lintf2_ether.pyType of Change
Proposed Changes
Change default of the --every option from 1 to 0.
The value of the --every option is parsed to the -dt option of the submitted Gromacs tools. In the Gromacs documentation (https://manual.gromacs.org/documentation/2018-current/onlinehelp/gmx-trjconv.html) it says about the -dt option:
However, when -dt is set to 1 and the spacing between frames is less than 1 ps, not every frame is processed, although t MOD 1 should be 0 for all (integer) values of t. When setting -dt 0, every frame is processed (although t MOD 0 should not be defined. However, 0 is the default value for -dt according to the docs).
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