| dc.description.abstract | Pine-MD (Protein INformation Extraction from Molecular Dynamics Simulation) is an in-house program designed to analyze the results of molecular dynamics simulations. It capcitity includes the analysis of molecular geometry, molecular conformation, inter-molecular structure, configuration, structure comparsion and classification, membrane properties, time-correlation property and statistics. This program uses text-based commands working under Linux environment, which is not user-friendly. Taking the fast development of web-based techniques, we setup a Lab Wiki and designed a program called Pine-MD GUI interacfacing with Pine-MD to integrate research resource and to assist the analysis of MD simulations.
With the aid of Lab Wiki, lab researchers can access the detailed and updated commands and methods of Pine-MD through the internet everywhere. Moreover, the program developers can easily update the commands and methods of their newly develpoed programs through Lab Wiki.
Pine-MD GUI is a newly developed program interfacing with Pine-MD working through Intenet browser. Pine-MD GUI has the following features making it user friendly: Its graphical interface reduced the text-command inputs by users; it guides users step-by-step for analysis which decreased the learning time of new users; in particular, its pop-up menu allows users to do atom section directly and friendly without any mistake. It improves the molecular simulation research effectively.
Using Pine-MD GUI, we analyze the miscroscopic properties of model bacterial membranes under Na+, Mg2+ and Ca2+ environments obtained from all-atom MD simulations. Results show that member under Ca2+ ion environments is packed more order that those of other two ions. Interestingly, Ca2+ ions prefer to locate around the phosphate groups different from those of other two ions.
| en_US |