[gmx-users] Resizing membrane (dopc, berger)

shayamra at post.tau.ac.il shayamra at post.tau.ac.il
Mon Apr 27 17:04:24 CEST 2009

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  
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,

More information about the gromacs.org_gmx-users mailing list