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#Mac tutorial for windows users pdf pdf#
#Mac tutorial for windows users pdf software#

The following tutorials cover multiple free-energy and potential-of-mean-force calculation methods using NAMD.

#Mac tutorial for windows users pdf pdf#

Download full text: PDF (977k)įree-Energy and Enhanced Sampling Methods Skeel, Laxmikant Kale, and Klaus Schulten. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. The physical concepts behind NAMD along with the program's design and algorithms are described in this publication that we recommend highly for study along with working through the above NAMD tutorial: Scalable molecular dynamics with NAMD.Please also see the NAMD Tutorial, the Stretching Deca-Alanine tutorial, and the Methods for calculating Potentials of Mean Force tutorial for content on steered molecular dynamics.The tutorials on Simulation of Water Permeation through Nanotubes and on Stretching Deca-Alanine both utilize IMD. For a brief introduction to running interactive molecular dynamics simulations, see the documentation here.Required tutorial files:, , individual files.

Tutorial works on Windows, Mac, and Unix/Linux platforms. These script-based facilities simplify the process of adding complex forces to systems and implementing boundary conditions. This tutorial is designed to guide users of VMD and NAMD in the use of the tclForces and tclBC scripts.Be sure you have the latest version of NAMD. These tutorials focus on NAMD specifically, although many others utilize it as well. Emad Tajkhorshid in November, 2007 is available here.

Video lectures: an introductory video, "Introduction to VMD Molecular Visualization and Analysis", recorded by Dr.

Selecting atoms by volumetric density values.

Coloring molecules by electrostatic potential, and other volumetric data.

Creating interactive 3-D PDF documents with VMD and Acrobat3D.

VMD outline rendering style inspired by the work of D.

Publication figure rendering using NVIDIA Gelato.

Publication figure rendering with Tachyon.

Guides participants in using VMD for visualizing results from molecular dynamics and electronic structure calculations, as produced by the CPMD program.

For users seeking to learn about a specific use of VMD.

Visualization and Analysis of CPMD data with VMD Be sure you have the latest version of VMD. These tutorials focus on VMD-specific features, although many others utilize VMD as well. Latest machine you have available while the tutorials will run on older

#Mac tutorial for windows users pdf software#

The user's computer, and installation of VMD, NAMD, and other required software asĭocumented at the start of each tutorial. Proceeding through a tutorial requires aĬopy of the tutorial text (in pdf or html format), tutorial files in place on The page below offers tutorials on tools created by TCBG,Īnd some tutorials from other groups. Speed, as a means of learning the best use of the VMD and NAMD Post and maintain tutorials that scientists can work through at their own For those who cannot attend these training events, we Through a variety of training opportunities, workshops, classes, presentationsĪnd demonstrations. TCBG strives to make its software accessible to the biomedical community