The determination of potentials of mean force for solute insertion in a lipid membrane by means of all-atom molecular dynamics simulations is often hampered by sampling issues. Recently, a multiscale method has been proposed to leverage the conformational ensemble of a lower-resolution model as starting point for higher resolution simulations. In this work, we analyze the efficiency of this method by comparing its predictions for propanol insertion into a lipid membrane against conventional atomistic umbrella sampling simulation results. The multiscale approach is confirmed to provide accurate results with a gain of one order of magnitude in computational time. We then investigate the role of the coarse-grained representation. We find that the accuracy of the results is tightly connected to the presence of a good configurational overlap between the coarse-grained and atomistic models—a general requirement when developing multiscale simulation methods.
Efficient potential of mean force calculation from multiscale simulations: Solute insertion in a lipid membrane / Menichetti, R.; Kremer, K.; Bereau, T.. - In: BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS. - ISSN 0006-291X. - 498:2(2018), pp. 282-287. [10.1016/j.bbrc.2017.08.095]
Efficient potential of mean force calculation from multiscale simulations: Solute insertion in a lipid membrane
Menichetti R.;
2018-01-01
Abstract
The determination of potentials of mean force for solute insertion in a lipid membrane by means of all-atom molecular dynamics simulations is often hampered by sampling issues. Recently, a multiscale method has been proposed to leverage the conformational ensemble of a lower-resolution model as starting point for higher resolution simulations. In this work, we analyze the efficiency of this method by comparing its predictions for propanol insertion into a lipid membrane against conventional atomistic umbrella sampling simulation results. The multiscale approach is confirmed to provide accurate results with a gain of one order of magnitude in computational time. We then investigate the role of the coarse-grained representation. We find that the accuracy of the results is tightly connected to the presence of a good configurational overlap between the coarse-grained and atomistic models—a general requirement when developing multiscale simulation methods.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione