I would like to determine bilayer repeat distance (d-spacing) from a simulation of a bilayer in water. This bilayer has water layer at the top. Followed by two monolayers and another single water layer.
I use local density profile (ldp)to determine the bilayer thickness. This can be calcluated from peak to peak distance from ldp.
By the way, if I want to determine the bilayer d-spacing I need to calculate a distance from a point in the first lipid monolayer to the third lipid monolayer from subsequent layer (this is imaginary lipid monolayer and it is assumend due to the application of periodic boundary condition).
I have given simple pictorial explanation on this below.
||water|L1|L2|water||water'|L1'|L2'|water'||
I want to calculate the distance from L1 to L1' (d-spacing). (the L1' is layer due to periodic boundary condition).
Since I have only two layers, it is impossible for me to determine the d-spacing from the ldp.
So I tried to figure out that the box dimension along Z - axis should represent the d-spacing.
Here I would like to get some suggestions or comments on this idea of determining the d-spacing.
If there is any other new suggestion I am eager to know too.
Thanks in advance.
Hi Vijay,
You are right in your assumption: d-spacing in your case is set by the system size along z axis, Lz. It becomes clear when you look at the right picture, and here is one that I found: http://www.rsc.org/ej/MB/2011/c0mb00149j/c0mb00149j-f2.gif
Thank you so much for your reply Maxim.
By the way I apreciate if you could send the citation for the paper where this picture is published.
Best regards
Sure, here is the link: http://pubs.rsc.org/en/content/articlelanding/2011/mb/c0mb00149j
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