New features in Desmond / Maestro include:
• GUI support for launching and analyzing metadynamics simulations
• Support for non-power of 2 processor topologies in standard workflows
• Script to support using custom charges in FEP calculations
• Maestro related improvements:
-Improved speed of trajectory viewer
-Improvements to trajectory analysis: atom-based root mean
square fluctuations (RMSFs) relative to a
reference structure; calculate RMSD for all pairwise
combinations of frames in a trajectory
-Can align on helices when building a membrane system
-Simulation event analysis can display statistics in a table
-Lambda Hopping for Relative Free Energy Perturbation
calculations to increase intramolecular
conformational sampling
• Enhancements to ‘MultiSim’:
- Support for metadynamics
- Support for internal restraints including flat bottomed
potentials
- Optional GCMC equilibration for FEP jobs
- Automated FEP analysis
• With this release of Desmond / Maestro the DESRES binary package can be installed directly into Schrödinger Suite 2011
The source code distribution includes instructions for compiling Desmond on GNU / Linux systems equipped with Intel/AMD x86/x86_64 processors. The executable files built from the source release run independently from the binary release integrated with Schrödinger’s Maestro Molecular Modeling environment. The source code distribution also includes structure and configuration files for the standard DHFR and ApoA1 benchmark systems.
Compiling and using Desmond optimally may prove challenging, but we look forward to working with you to provide the widest possible support for different computer systems and architectures. The distribution archive contains release notes detailing changes from previous versions. By far, the most significant changes are in how Desmond applications are configured, though there are a few new features, including support for simulations with all bond lengths constrained and additional functional forms for enhanced sampling.
Also included with the release is an updated User’s Guide and Tutorial (you can also find these at https://www.deshawresearch.com/resources.html). We recommend that you look these over for further information and check the “Known Issues” file included with the binary distribution for undocumented issues and problems. We would like to encourage you to visit our Desmond MD Users site (https://sites.google.com/site/desmondmdusers/home), where you can find FAQs, workshop information, and a number of sample simulations for download.
