Hello dear GROMACS users,
Lately I have been trying to user dopc membrane, using Berger united
atoms and I am confounded by a problem regarding the size of the
membrane.
The original membrane from the website is X Y Z (including 128
lipids). Now I would like to multiply the membrane by 1.5 and I cannot
find how.
Is there a (relatively) simple way of doing it?
I have tried several approaches:
1) genconf -f dopc128.gro -o dopc_new.gro -nbox 2 2 1
This option can only multiply the by *whole* integer numbers.
2) genconf -f dopc128.gro -o dopc_new.gro -box 1.5X 1.5Y Z # (X and Y
multiplied by 1.5, Z is unchanged).
The dopc_new.gro file will contain X1.5 molecules, but the water
molecules will extend much further than the lipid molecules. So now
there's a small "vacuum" in the gap between upper/lower leaflets of
the membrane in which water can invade.
I would much like to be able to use X1.5 and not X2 since that would
"save" me a whole lot of water/other molecules in the Z-axis, and
therefore simulation time too.
Thanks in advance,
-Shay
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