Interesting thoughts and tutorials from the White Lab at the University of Rochester.. Topics include mathematical modeling, programing, computational chemistry and statistics. This is a continuation of random posts from my time in grad school and post-doc. Back then, this was called Crows and Cats Blog. Some of those older are best viewed at my old url: crowsandcats.blogspot.com.

VMD render preferences

Here are some notes on my preferences for rendering with VMD’s tachyon. For example, this comparison of some proteins was made with the Space Filling method below:

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VMD movie script

Here are two example scripts for making movies in VMD. The first is shown below and the other controls the camera to follow an interesting part of the simulation.

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EDS Lammps Coordination Number

This tutorial will show you how to reproduce the method in the recent White et al. water AIMD paper (White et al., 2017). The goal of the method is to minimally bias a water simulation to match a reference RDF. We will first convert a reference RDF into a set of reference scalar coordination number moments. Then, an NVT simulation is run to find a minimal bias which causes the coordination numbers to match their reference values. It won’t be covered here, but the bias can then be used to run NVE simulations or in conjunctino with other free-energy methods. This tutorial will use classical simulations in Lammps instead of AIMD in CP2K so that results can be obtained in a reasonable amount of time.

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