Bignose's box of stuff

In this entry I'd like to document something that I get asked by few people and for which I assembled a script several years ago. I'd like to put it here for everyone to use (and perhaps for some to contribute, just a wish). In the past I've worked on something called "Path Collective Variables" (PCVs) which are some useful descriptors that are used in enhanced sampling (umbrella sampling, metadynamics, steered-MD and others).  The essence of the PCVs is that if you have a trajectory, being it true or fictitious, of a reactive event you can use this as a blueprint, a sort of "track" and ask the system to walk over it using some enhanced sampling method so that you will be able to measure the thermodynamic force along it and calculate the free energy.  Getting a rough reactive trajectory can be simple in many cases. One can put a harmonic restraint on the coordinate of your target (say "state B") structure and pull the system toward it wi...

  Introduction In the past I've been using the Schrödinger Molecular Modeling suite quite a bit and I had the chance of working with some talented guys that have taught me a great deal about how that's working.  One of the hidden gems of it is the ability of doing enhanced sampling using Desmond molecular dynamics code on GPU. Desmond is a great piece of software but it is closed source and the users base consists mostly of people who are using it via the Maestro GUI to run FEP+, MD or some pre-canned metadynamics workflows. Therefore is no surprise there's very little out there on how to access many capabilities which sits there.  In this blog entry I'd like to explain a little of how it works and give you an initial glimpse of the capabilities of it.  The case below is worked up using the version 23-1 of the suite but this is a part of the code which is rarely touched so it should be fairly retrocompatible (within a limit). This blog entry is for you if you have ev...

Embedding code into the blog I can embed a html generated with http://hilite.me/ 1 print ( 'hello world!' ) Equations in google sites Equations go with again as an  embeeded HTML object. Here is a useful link  (useful because has some encodings) and here is another link . The equation is produced as an image by a link like: http://www.google.com/chart?cht=tx&chf=bg,s,FFFFFF00&chco=000000&chl=e^z=\sum^{\infty}_{n=0}\frac{z^n}{n!} Where you can clearly see the underlined part is Latex. And it needs to get embedded in this way <img src="http://www.google.com/chart?cht=tx&chf=bg,s,FFFFFF00&chco=000000&chl=e^z=\sum^{\infty}_{n=0}\frac{z^n}{n!}" />  And here is a test