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

shayamra at post.tau.ac.il shayamra at post.tau.ac.il
Mon Apr 27 18:12:27 CEST 2009

Hi Chris,

Thanks a lot for your quick reply - I will try to equilibrate.

Quoting chris.neale at utoronto.ca:

> The simplest way to get around what you describe is to continue with  
> your procedure and then equilibrate your membrane. Use semiisotropic  
> pressure coupling and you will have what you want after 20-50 ns.  
> You could alternatively build and equilibrate your own membrane, but  
> this will require approximately the same amount of simulation time.
> I wouldn't be surprised if you can fix this problem as a side-effect  
> of the inflategro script. You could also use the make-hole version  
> of gromacs 3.1.4 to keep your waters from entering the membrane  
> during equilibration. However, you should be easily able to  
> equilibrate your membrane within one week of wall time so the  
> brute-force method may be faster for you than learning some new tools.
> Chris.
> -- original message --
> 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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