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DOPC Box vector
- 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
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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