Efficient free energy calculation of water across lipid membranes.
An efficient free energy (FE) calculation of a water molecule to go across lipid membranes is presented. Both overlapping distribution and cavity insertion Widom methods are complementarily used. The former is useful for a dense region where water molecules are found, i.e., from the interfacial to bulk water region, while the latter works well in the low density region, i.e., the hydrocarbon region. Since both methods evaluate the excess chemical potential of water, the obtained FE profile is free from the fitting problem usually arisen when a FE difference method is used. A diphytanyl phosphatidylcholine bilayer is used for our test calculations. An excellent and fast convergence of the chemical potential is obtained when each method is applied for the appropriate region. The estimated FE barrier using the Ewald method for the electrostatic interaction is approximately 7.2 kcal/mol, which is higher than that using the interaction cutoff of 20 A by about 0.9 kcal/mol.
Shinoda
Keiko
K
Research Institute for Computational Sciences (RICS), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 2, Umezono 1-1-1, Tsukuba 305-8568, Japan.
Shinoda
Wataru
W
Mikami
Masuhiro
M
D008051:Lipid Bilayers / Q000737:chemistry*; D008956:Models, Chemical; D010713:Phosphatidylcholines / Q000737:chemistry; D055672:Static Electricity; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
D008051:Lipid Bilayers; D010713:Phosphatidylcholines; D014867:Water; C021016:1,2-diphytanoylphosphatidylcholine