AllosMod is a web server to set up and run simulations based on a modeled energy landscape that you create. Carefully designed energy landscapes allow efficient molecular dynamics sampling at constant temperatures, thereby providing ergodic sampling of conformational space. Use AllosMod to:
The AllosMod server runs in two modes: 1) single landscape and 2) batch jobs to set up many
simulations at once. By creating a single landscape, the server will create input files that can
be used to submit batch jobs. AllosMod will set up many short
simulations for each landscape. There are two types of sampling: 1) constant temperature
molecular dynamics, which will be completed overnight on a single processor on the
user's computer (using MODELLER) or 2) quick, unequilibrated simulations performed on our servers
within minutes to hours. Sampling is achieved efficiently by starting each simulation at different
points in conformational space and by storing the energies in memory.
AllosMod has several options for conformational sampling and contains tools for simulation analysis. For more details click on the "About AllosMod" link above and read the paper listed below.
***NEW*** The AllosMod server is integrated with the FoXS server for rigid body modeling of small angle X-ray scattering profiles. Our combined server is AllosMod-FoXS.