Paper Citing NAMD - Abstract
Gullingsrud, J.; Babakhani, A.; McCammon, J. A.
Computational investigation of pressure profiles in lipid bilayers with embedded proteins
MOLECULAR SIMULATION, 32:831-838, AUG-SEP 2006
The distribution of surface tension within a lipid bilayer, also referred to as the lateral pressure profile, has been the subject of theoretical scrutiny recently due to its potential to radically alter the function of biomedically important membrane proteins. Experimental measurements of the pressure profile are still hard to come by, leaving first-principles all-atom calculations of the profile as an important investigative tool. We describe and validate an efficient implementation of pressure profile calculations in the molecular dynamics package NAMD, capable of distinguishing between internal, bonded and nonbonded contributions as well as those of selected atom groups. The new implementation can also be used in conjunction with Ewald summation for long-range electrostatics, improving the accuracy and reproducibility of the calculated profiles. We then describe results of the calculation of a pressure profile for a simple protein-lipid system consisting of melittin embedded in a DMPC bilayer. While the lateral pressure in the protein-lipid system is nearly the same as that of the bilayer alone, partitioning of the lateral pressure by atom type revealed substantial perturbation of the pressure profile and surface tension in an asymmetric manner.
