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dockonsurf / modules @ 3c26e233

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# Date Author Comment
3c26e233 02/14/2020 06:55 pm Carles Marti

Enabled the possibility to do coadsorption by checking collision with neighbor lists. Removed the coadsorption box option. Included the increase in height to prevent collision as last option when rotation doesn't work

0d7be691 01/22/2020 02:58 pm Blanck Sarah

adsorption takes into account the z of the surface atom and not the highest point of the surface

3ba3c134 01/21/2020 03:14 pm Carles Marti

In the case of launching with the only-refinement flag and that an analyse / relaunched_calculation directories already exists, the user is asked whether to delete or not these directories before the script puts itself to run in background; Solves #2729

aa4d21b6 01/20/2020 02:43 pm Carles Marti

Merge branch 'master' of

2137c2de 01/20/2020 02:42 pm Carles Marti

Now modules/ works even if the surface file ends with blank lines; fixes #2727

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.

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