[gmx-users] Increasing sigma

[Hannes Loeffler]

On Fri, 5 May 2017 15:09:09 +0200
Pallavi Banerjee <pallavisept at students.iiserpune.ac.in> wrote:

> I intend to perform thermodynamic integration of my system, but not to
> calculate the free energy. I want to gradually increase the radius of
> the carbon atoms of the alkyl chains of my lipid molecules. This is
> because I could see a hole forming in my lipid bilayer along the
> edges of the simulation box and the water molecules pass through it.
> 
> Once the system with the bigger radius equilibrates, I would then
> gradually beat down the radius to the original value.

I don't think that would solve your problem.  You would be pretending
that your lipids (and thus the box size) are larger then they are but
what the bilayer really wants to do is to contract.  And water is very
quick in filling the voids.  So if you decrease the radii again you may
just be back where you have started because your lipids still need to
attain the desired density.