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DNA tutorial
- martin.calvelo
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6 years 11 months ago #7270
by martin.calvelo
DNA tutorial was created by martin.calvelo
Hi everyone,
I'm doing the DNA tutorial and I have a question related with one option of "mdrun". In the tutorial it is said that:
"Note that with the elastic network the domain cell size needs to be kept fairly large (option -rdd 2.0)."
My question is: this value for -rdd (2.0) is it directly related with the box size? I mean, if the box size were bigger, for example changing the distance between the DNA molecule with the edges of the boxes using -bt 2.0 (instead of editconf -f cg-1bna.pdb -d 1.2 -bt dodecahedron -o box.gro in the step 5), should the value for -rdd be different?
Thanks in advance
Martin
I'm doing the DNA tutorial and I have a question related with one option of "mdrun". In the tutorial it is said that:
"Note that with the elastic network the domain cell size needs to be kept fairly large (option -rdd 2.0)."
My question is: this value for -rdd (2.0) is it directly related with the box size? I mean, if the box size were bigger, for example changing the distance between the DNA molecule with the edges of the boxes using -bt 2.0 (instead of editconf -f cg-1bna.pdb -d 1.2 -bt dodecahedron -o box.gro in the step 5), should the value for -rdd be different?
Thanks in advance
Martin
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- bart
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6 years 3 months ago #7488
by bart
Replied by bart on topic DNA tutorial
Heya,
Pretty late, but maybe someone has the same question.
The answer is no, the rdd is the length at which bonded interactions are still considered to occur, this is important for balancing communication and parallelization (therefore directly related to the domain decomposition).
Pretty late, but maybe someone has the same question.
The answer is no, the rdd is the length at which bonded interactions are still considered to occur, this is important for balancing communication and parallelization (therefore directly related to the domain decomposition).
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