On 1/10/13 11:37 PM, Kieu Thu Nguyen wrote:
Thank Justin and Peter so much !
Can i make a new box (it's size is not a multiples of the size of the
previous box) from a smaller lipid bilayer box ?
I don't see genconf -nbox can do that.
genbox -cs old_lipids.gro -box x y z -o new_lipids.gro
Just make sure you get a sensible number of lipids per leaflet.
-Justin
On Fri, Jan 11, 2013 at 9:20 AM, Peter Lai <[email protected]> wrote:
Kieu Thu Nguyen <[email protected]> wrote:
Dear All,
I see in MD simulations, the number of lipids is 128 or multiples of
128.
Can someone tell me why ?
Whether can i choose another number of lipids ?
Thanks in advance !
KT
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probably because they are using original 128-lipid coordinates from
someone like tieleman or klauda. You can use any arbitrary # of lipids
appropriate to the size of your intended system (like scaling it so that an
embedded protein is shielded by lipids from its periodic image)
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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