[gmx-users] Increasing sigma

[Pallavi Banerjee]

Hi gromacs users,

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.

Could someone suggest ways to do it in gromacs?

Thanks in advance!

Best,
Pallavi Banerjee