[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)
reach.anirban.ghosh at gmail.com
Fri Apr 27 15:19:43 CEST 2012
On Fri, Apr 27, 2012 at 6:31 PM, Bala S <think_beyond at aol.com> wrote:
> Sorry for that.. Now I could realize it.
> Following up.. I have done further iterations with inflategro and reached
> 0.62 nm^2 which similar to what you have explained in the tutorial.
> Now, I could see the lipid bilayer really shrinked and no SOL molecules are
> seen in between. Now the issue I would like to have clarification on is
> only 163 SOL molecules were added up and down which looks very scarce for
> the simulation.
> What is the solution?
First visualize and see whether the hydrophilic ends of the lipid bilayer
and your protein's part on either side of the bilayer (like a GPCR's intra
and extra cellular ends) are well immersed in the water box. If not, you
can increase the solvation box along the z-axis by increasing the z value
for -box option in editconf (keeping x and y values same).
> Bala S
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