# [gmx-users] How to make a lipid bilayer with specific dimensions?

I don't think that this is currently causing anybody any problems, but note that genbox is going to cut any lipids that cross out of the central unit box (either because genbox is unaware of PBC or because these lipids now clash across PBC).
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Therefore:```
```
genbox -cs popc128a.pdb -o popc_new.pdb -box 9.6 9.5 6.919

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will give you a bilayer that gets solvated with a water defect around the edges of the initial unit cell and that, after 10 - 200 ns of simulation, gives you an equilibrated bilayer (without water defect) that is much smaller than x=9.6, y=9.5.
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To get what you want, you need to either start your bilayer with larger x and y (calculate area per lipid in 9.6*9.5 to figure out how many lipids you should have and keep running genbox until you get that), or perhaps a run through inflategro might do it.
```
Chris.
--original message --

[gmx-users] How to make a lipid bilayer with specific dimensions?
Justin A. Lemkul jalemkul at vt.edu
Mon Sep 27 13:00:32 CEST 2010

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NG HUI WEN wrote:
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```Dear gmxusers,

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I am trying to make a lipid bilayer with specific dimensions using gromacs. So far, I have got up to:
```

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2) Use genconf ?f popc128a.pdb ?o popcx2.pdb ?nbox 2 2 1 to multiply the lipid in the x and y axis. The resultant output was a lipid with box vectors 12.478 , 12.359 and 6.919 (nm)
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My ultimate aim is to generate a POPC bilayer with the dimensions 9.600 9.500 and 14.000. Currently, the lipid bilayer is too big. I
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Too big?  If you're using either of the two coordinate files above
(popc128a.pdb, popcx2.pdb), they should be too small.

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would like to ?crop? the excess lipids to the required size if at all possible. I tried using editconf ( a bit of a long shot) to make a new box size. The new structure file has a CRYST1 of 9.600 9.500 and 14.000 but when I view it with VMD, it is not any smaller than before.
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Do I have to use other software to achieve this? If so, I?d really appreciate some pointers.
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You can do this in three steps. If your goal is to have a single lipid bilayer
```in the middle of the box, with water around it:

genbox -cs popc128a.pdb -o popc_new.pdb -box 9.6 9.5 6.919
editconf -f popc_new.pdb -o popc_new2.pdb -c -box 9.6 9.5 14
genbox -cp popc_new2.pdb -cs spc216.gro -o solv.pdb

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The reason you need three steps is that if you supply a z-dimension of 14 in the first genbox command, at least two full bilayers (or some fraction close to it) will be placed in your box. If that's your goal, then this can be done in one step.
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-Justin
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``` Thanks!

<<

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Email has been scanned for viruses by UNMC email management service <http://www.nottingham.edu.my>
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>>

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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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