Hello all,
I am trying to do free energy verification by thermodynamic integration on Martini 3. I need a coordinate file for octanol, beacuse the reference partition coefficient is calculated with octanol. I obtained one gro file from the example applications part on martini’s official site. But that file defines octanol as a 2 bead molecule whereas in the solvents.itp file it is defined with 3 beads. So, when I try to use that file for my simulation it adds a number of solvents which I cannot define to the topology file because of the bead number mismatch. Is there any way I can obtain the correct octanol coordinate file for martini 3. I searched for some articles but couldn’t find any. I’d greatly appreciate all the help.
Best regards,
Yıldız Kırbaç