[gmx-users] problem in increasing lipid bilayer size and to know about net charge on protein

Justin A. Lemkul jalemkul at vt.edu
Thu Apr 9 12:09:53 CEST 2009

nitu sharma wrote:
> Hi justin
>                   Thanks for tutorial of membrane protein simulation its 
> very useful for us . But  I want to ask  two basic question -
> 1.The lipid bilayer I have downloded from teleman sir website is so 
> small in comparision with my protein the suitable box vector for my 
> protein is  13nm 13nm and 5nm w.r.t XYZ but the lipid bilayer
> vector is 6.52270 ,6.54870 ,6.03310. So I want to increase the size of 
> lipid bilayer w.r.t my protein that means it should be same size.
> can you suggest me how "genconf "command useful in doing this .

Well, you already know that genconf is necessary, now read about how to use -nbox.

> 2. I want to know the net charge present on my protein can u suggest me 
> how can it become possible .

pdb2gmx or grompp will tell you in their output, or look at the qtot column in 
your .top.


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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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