Molecular dynamics is an important simulation tool for structural biology. In lipid membrane research, molecular dynamics is vital because it can access the atomic features of membranes that are difficult to obtain experimentally. CD ComputaBio can provide you with the solution to simulate lipid membranes on a computer, including the initial membrane system setup to the actual analysis. Most of the tasks described here are performed using the Gromacs simulation suite, which is a widely used software for molecular modeling and simulation. One of the most studied lipid species has been the single-component lipid bilayer composed of DPPC.
Figure 1. Lipid molecular dynamics simulation service.
A new protocol has been developed for comparing the structural properties of lipid bilayers determined by simulation and by diffraction experiments. It is now possible to strictly test molecular dynamics simulations' ability to reproduce experimental data. This model-independent method includes analyzing the data of the molecular dynamics double-layer simulation in the same way as the experimental data by determining the structural factors of the system and determining the entire cross-layer scattering density distribution map by Fourier reconstruction. Using the unified atomic GROMACS and all-atomic CHARMM22/27 force fields and GROMACS and NAMD, under constant pressure and temperature set, the poleoylphosphatidylcholine bilayer molecule under 66% RH (5.4 water/lipid) was tested using nanosecond molecular dynamics simulation software package. The quality of the simulated double-layer structure can be evaluated by comparing the simulation and experimental results. The thickness of the double layer, area/lipid, distribution of individual molecular components, continuous and discrete structural factors, and overall scattering density distribution can also be determined.
Figure 2. Molecular dynamics simulation process.
|Project name||Lipid molecular dynamics simulation service|
|Samples requirement||The initial structure of the Lipid, PDB ID, etc.|
|Timeline||Depends on the time you need to simulate.|
|Deliverables||We provide you with raw data and calculation result analysis service.|
CD ComputaBio provides corresponding lipid molecular dynamics simulation services. The CD ComputaBio team has been working in this field for more than ten years and has published his findings in top scientific journals. Our team of experts can provide up to one millisecond of simulation time for the system you choose, so you do not have to worry about technical issues. We can also analyze these results for you.