normal -rdd

  • syahidah
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8 years 3 months ago #1039 by syahidah
-rdd was created by syahidah
Dear all,

may i know what makes us need to add -rdd,
Because when i run the self-assembly of DSPC using gromacs 4.0, 4.5.5 and 4.5.4 in fedora 16,
i didn't add -rdd, the bilayer was formed.

However, when i run the same process (same input,same command) using gromacs 4.5.5 in ubuntu 12.04LTS, we were asked to add -rdd 0.14, then only the production run can be simulated...

may i know what makes we need to add -rdd?
anyone here have any idea?

your reply is greatly appreciated..

best,
syahida

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8 years 3 months ago #1043 by djurre
Replied by djurre on topic -rdd
-rdd concerns: "The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates".

Since in Martini topologies bonded interactions can stretch over a long distance, due to long bond lengths, mdrun sometimes estimates rdd to short. This means that if two atoms that are bonded (bond, angle, dihedral) move further apart then the estimated rdd and are on different compute nodes, mdrun can't find these atoms and the system crashes.

That is why it is better to set rdd a bit bigger, typically 0.14-0.16 should be enough. This will not influence your results. It could limit the number of compute nodes you can use, but since the number of beads per volume in Martini is much lower then atomistic, the scaling will go down much earlier.

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8 years 3 months ago #1044 by syahidah
Replied by syahidah on topic -rdd
Dear djurre,

Thank you so much for the explanation..

got it=)

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