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normal box of dppc vesicle

  • msaeedi
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10 years 8 months ago #1828 by msaeedi
box of dppc vesicle was created by msaeedi
Hi,
i studied dppc_vesicle.gro in example part. the last line that is about box vector is
22.40597 21.12889 18.29325 0.00000 0.00000 7.47458 0.00000 -7.47458 10.56446
it explains that dppc vesicle is in the cubic box but i think that it is wrong.please tell me what type of box is used in this example?

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10 years 8 months ago #1829 by djurre
Replied by djurre on topic box of dppc vesicle
You are right, the dppc_vesicle.gro is not a cubic box. The statement on the download page was wrong: DPPC is in an octahedral box, POPE is in a cubic box. I've corrected it, thanks for letting us know!

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10 years 8 months ago #1830 by msaeedi
Replied by msaeedi on topic box of dppc vesicle
Thank for your reply.
i try to inset 877 dppc and 61552 cg water in octadedron box with 22.40597 21.12889 18.29325 size box, but in the gro file the water dont occupy whole port of box. is it wrong? what can i do to inset water in whole part of box?

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10 years 8 months ago #1831 by djurre
Replied by djurre on topic box of dppc vesicle
You could try to use a smaller box, a larger -vdwd for genbox or simulate the system untill the 'vacuum' has disappeared.

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