[gmx-users] convergence of bilayer simulation

[Prasanth G, Research Scholar]

Dear Roshan,
Thank you for your response. I thought that the lipid also behaves as a
solvent in the case of membrane simulation. we even try to make sure the
set temperature (starting from equilibration) is beyond the phase
transition temperature. I wonder what sort of impact this will have on rmsd
and how effective it can be, to know weather the bilayer is equilibrated or
not.
I will surely give it a try.
For now, I have calculated the APL (Area per lipid) and found that it was
around 62 Angstrom (square). I am working on POPC, and this value is close
to the reported APL of 65 Angstrom (square).
I have also checked the dimensions of the box along the simulation and
found it to not fluctuate much.
I am hoping this would be sufficient.