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Frequently Asked Questions

What's new in YASARA dynamics?

YASARA Dynamics contains YASARA Model and adds support for molecular simulations. Beside the YASARA NOVA Force Field and the new highly accurate YAMBER force fields, you can use other well known MD force fields like AMBER, and run accurate all-atom MD simulations in aqueous solution with Particle Mesh Ewald longrange electrostatics.

Can I use other force fields with YASARA dynamics?

In addition to YASARA's own force fields ( NOVA , YAMBER) you can use other well known MD force fields like AMBER, and run accurate all-atom MD simulations in aqueous solution with Particle Mesh Ewald longrange electrostatics. YASARA Dynamics is not a "black box" with input and output files, but shows the MD simulation in real-time on screen.

What is YASARA used for?

YASARA. Yet Another Scientific Artificial Reality Application ( YASARA) is a computer program for molecular visualising, modelling, and dynamics. It has many scientific uses, as expressed by the large number of scientific articles mentioning the software. The free version of YASARA is well suited to bioinformatics education.

How does the YASARA simulation report work?

YASARA runs for each block the md_analyze macro and creates in the end a single report containing detailed information about the system, e.g. energies, RMSDs, hydrogen bonds per block. By default the simulation snapshots are split into 3 blocks, so the second and third block can be compared to see if convergence has been reached.

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