| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/chemteam/gmx_check/gmx_check/2022+galaxy0 (this tool) |
| gmx_check |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| gromacs | 2022 | package |
| Additional information about this tool |
#if $input_file.calculate_select == "info_traj":
ln -s '$input_file.traj_file' './traj.$input_file.traj_file.ext' &&
gmx check
-f './traj.$input_file.traj_file.ext'
&> '$out_info_traj'
#elif $input_file.calculate_select == "compare_traj":
ln -s '$input_file.traj_file' './traj1.$input_file.traj_file.ext' &&
ln -s '$input_file.traj_file2' './traj2.$input_file.traj_file2.ext' &&
gmx check
-f './traj1.$input_file.traj_file.ext'
-f2 './traj2.$input_file.traj_file2.ext'
$input_file.rmsd
-tol '$input_file.rel_tol'
-abstol '$input_file.abs_tol'
&> '$out_compare_traj'
#elif $input_file.calculate_select == "info_struc":
ln -s '$input_file.struc_file' './struc.$input_file.struc_file.ext' &&
gmx check
-c './struc.$input_file.struc_file.ext'
-vdwfac '$input_file.vdwfac'
-bonlo '$input_file.bonlo'
-bonhi '$input_file.bonhi'
&> '$out_info_struc'
#elif $input_file.calculate_select == "info_ener":
ln -s '$input_file.ener_file' './ener.$input_file.ener_file.ext' &&
gmx check
-e './ener.$input_file.ener_file.ext'
&> '$out_info_ener'
#elif $input_file.calculate_select == "info_ind":
ln -s '$input_file.ind_file' './index.$input_file.ind_file.ext' &&
gmx check
-n './index.$input_file.ind_file.ext'
&> '$out_info_ind'
#elif $input_file.calculate_select == "compare_ener":
ln -s '$input_file.ener_file' './ener1.$input_file.ener_file.ext' &&
ln -s '$input_file.ener_file2' './ener2.$input_file.ener_file2.ext' &&
gmx check
-e './ener1.$input_file.ener_file.ext'
-e2 './ener2.$input_file.ener_file2.ext'
-tol '$input_file.rel_tol'
-abstol '$input_file.abs_tol'
-lastener '$input_file.lastener'
&> '$out_compare_ener'
#else:
ln -s '$input_file.top_file' './top1.$input_file.top_file.ext' &&
ln -s '$input_file.top_file2' './top2.$input_file.top_file2.ext'&&
gmx check
-s1 './top1.$input_file.top_file.ext'
-s2 './top2.$input_file.top_file2.ext'
-abstol '$input_file.abs_tol'
&> '$out_compare_topol'
#end if
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_file|traj_file: nvt.xtc input_file|calculate_select: info_traj |
name: value |
nvt.xtc value |
| Test-2 |
input_file|traj_file: nvt.xtc input_file|traj_file2: npt.xtc input_file|rmsd: True input_file|rel_tol: 0.1 input_file|abs_tol: 0.1 input_file|calculate_select: compare_traj |
name: value |
nvt.xtc npt.xtc value |
| Test-3 |
input_file|struc_file: minim.gro input_file|vdwfac: 0.8 input_file|bonlo: 0.4 input_file|bonhi: 0.7 input_file|calculate_select: info_struc |
name: value |
minim.gro value |
| Test-4 |
input_file|ener_file: minim.edr input_file|calculate_select: info_ener |
name: value |
minim.edr value |
| Test-5 |
input_file|ind_file: index.ndx input_file|calculate_select: info_ind |
name: value |
index.ndx value |
| Test-6 |
input_file|top_file: npt.tpr input_file|top_file2: npt2.tpr input_file|abs_tol: 0.1 input_file|calculate_select: compare_top |
name: value |
npt.tpr npt2.tpr value |
| Test-7 |
input_file|ener_file: minim.edr input_file|ener_file2: outp.edr input_file|rel_tol: 0.1 input_file|abs_tol: 0.1 input_file|lastener: Pressure input_file|calculate_select: compare_ener |
name: value |
minim.edr outp.edr value |