normal RDD question

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4 months 3 weeks ago #8194 by daniloboskovic
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I have a crRNA of a CRISPR Molecule that i want to simulate (ssRNA with loops + hybridized to another ssRNA). Should i use RDD 2.0?

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4 months 3 weeks ago - 4 months 3 weeks ago #8200 by riccardo
Replied by riccardo on topic RDD question
I do not know what the default RDD (aka, -rdd flag of gmx mdrun) settings are for RNA. Did you check/do the RNA tutorial: cgmartini.nl/index.php/tutorials-general...ial-martini-rna-gmx5 or checked the paper: www.cell.com/biophysj/fulltext/S0006-3495(17)30612-4 ?

Note also some discussions in this forum about RDD:
md.chem.rug.nl/index.php/component/kunena/11-tutorial/1039-rdd
md.chem.rug.nl/index.php/component/kunen...02-an-error-with-rdd
Last edit: 4 months 3 weeks ago by riccardo. Reason: Link was wrong

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4 months 3 weeks ago - 4 months 3 weeks ago #8203 by daniloboskovic
Replied by daniloboskovic on topic RDD question
Thanks for reply. In RNA it states 2.0 but i have a RNA-protein simulation. Also my RNA is as stated very complex and an advice is needed rather than a literature search reply.
Last edit: 4 months 3 weeks ago by daniloboskovic.

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4 months 3 weeks ago #8205 by riccardo
Replied by riccardo on topic RDD question
If RNA requires 2.0 according to your search then you should stick to that. This won't affect your protein (see, e.g., what I linked earlier), but will just limit the number of processors on which you can run the simulation, i.e., you will get less performance.

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4 months 2 weeks ago #8208 by bart
Replied by bart on topic RDD question
To be more precise it only affects your system at the maximum domain decompostition you can achieve. So unless you are using the absolute maximum domain decomposition, you will not notice any difference in performance.

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