[gmx-users] genbox

Derrick Guang Yuh Lee k24dgyl at mun.ca
Tue Aug 10 19:07:08 CEST 2004

just curious, but does the, assumably, the gro file you used w/ genbox to
multiple your molecule have a box size? like, if the gro file
theoretically has a box size that is relatively large in comparison to
the molecule, then genbox's stacking could explain the distance in between
the heads of your molecule. that's all i can say... hope you figure it

 - derrick

 derrick Lee
 faculty of Science
 Memorial University of Newfoundland
 k24dgyl at mun.ca / derrickglee at hotmail.com

"a teacher is never a giver of truth - he is a guide, a pointer to the
truth that each student must find for himself. a good teacher is merely a
                                                              - bruce lee

On Tue, 10 Aug 2004, Dinesh Pinisetty wrote:

> Hi all,
>        i tried to generate a monolayer of a membrane of 128 molecules.
>  I took a single molecule with fifty atoms and then I used genbox to
> multiply it to 128,I got monolayer but the head to head distance is too
> weird, though i give 0.7 as head to head distance they look very far
> apart.when I read manual about genbox I understood that it stacks
> simulation boxes with molecules and thus they are very far apart,am I right
> in this.....
>  Now please anyone suggest how to get the distance between molecules very
> close with head to head distance very low and all the molecules being in
> same simulation box.Can I use genbox multiply and allow all the molecules
> being in same box with head to head distance what i mention.........If yes
> how,what are staements to be given.
>  Please help me out in this regard..............
> Thanking you,
> Dinesh........
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