DOPC Box vector

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robrob2013
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10 years 10 months ago #1705 by robrob2013

DOPC Box vector was created by robrob2013

Dear All,

I had already completed the tutorial for the DSPC Bilayer. I would like to ask if there is such an explanation why the dimension of the box is set at 7.5 x 7.5 x 7.5?

"genbox -ci dspc_single.gro -nmol 128 -box 7.5 7.5 7.5 -try 500 -o 128_noW.gro"

or is there any literature that discuss this?

Thank you very much.
Cheers to all the GROMACS users!

Robby

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djurre
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10 years 10 months ago #1706 by djurre

Replied by djurre on topic DOPC Box vector

A box of that volume has sufficient space to accommodate 128 lipids + enough water to get a nice bilayer. More or less water means you might get other lipid structures (eg inverted hexagonal or bicelles). Also it is cubic so the probability of forming a bilayer in any direction is the same.

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robrob2013
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10 years 10 months ago #1707 by robrob2013

Replied by robrob2013 on topic DOPC Box vector

I see. Again, Thanks djurre for the usual help.

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