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. -- Gromacs Users mailing list
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