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dockonsurf / modules @ e75a54af

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# Date Author Comment
e75a54af 01/16/2020 11:32 am Carles Marti

Removed the possibility to remove hydrogens from the RMSD check. Changed also the RMSD check to not include atom permutations. This should speed up the RMSD check process, while distinguishing different H spatial position when important like hydrogen bond formation

088cfdb3 01/07/2020 04:09 pm Carles Marti

Added the possibility to control the rmsd threshold in the check of different conformers

afd5ca03 01/06/2020 04:58 pm Carles Marti

Added the possibility to remove hydrogens during the calculation of RMSD of generated structures

76cb4d88 12/31/2019 06:17 pm Carles Marti

Sets the initial step number of the refinment calculation not to be conserved from the lower precision stage (ie. it starts always at 1); Fixes #2706

36f722bc 12/17/2019 10:05 am Carles Marti

Added the possibility to carry out coadsorption. By adding the -b option, when the surface file already contains an adsorbed molecule, it creates a box around it to prevent the second adsorbate to overlap the first.

454be75d 11/27/2019 04:08 pm Carles Marti

Now dockonsurf takes the geometry of the optimized most stable conformer; fixes #2676

a63e902e 11/27/2019 03:00 pm Carles Marti

Corrected a typo in the comments

459ffbcd 10/17/2019 04:43 pm Marti Aliod Carles

Now it is possible to call dockonsurf.sh script with options. These include: Usage: dockonsurf [OPTION]=PATTERN -h, --help display this help text and exit. -q=NUM, --max-qw=NUM allows a maximum of NUM jobs on 'qw' status. -a, --only-ads carry out only adsorption part. -i, --only-isolated carry out only isolated molecules part. -r, --only-refinement carry out only refinement of adsorbed structure.

f43a1b4c 10/15/2019 11:58 am Marti Aliod Carles

The check for running jobs has changed from checking the job name to checking the job num id.

d3aa7749 10/09/2019 03:14 pm Marti Aliod Carles

fe_change.sh now expects a surface xyz file ended with a carriage return character

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