Native contact (Q) biasing in GROMACS and plumed2

Fraction of native contacts is a pretty darn good coordinate for looking at protein folding, definitely when it comes to small proteins. Just have a look:

http://www.pnas.org/content/110/44/17874.abstract

Fraction of native contacts can be used to analyze long, unbiased MD runs – like those from DESRES – or in biasing simulations. But how does it fare when used in biasing? Well I don't know – but you can now find out by yourself! Either in umbrella sampling or metadynamics – or a method of your choice that doesn't use energy as your collective variable.

Here, I'm happy to report that I incorporated an implementation of native contact CV into plumed2 – an enhanced sampling package that can be used with a number of popular MD simulation engines. The pull request is now closed https://github.com/plumed/plumed2/pull/177 and it's likely that the next release of plumed2 will include this.

"Tutorial" is a regression test in plumed2 sources  regtest/basic/rt29/ which shows a simple plumed input for a trp-cage protein.

Credits: Robert Best for writing the original gromacs-only implementation, Wenwei Zheng for the draft plumed2 implementation, Giovanni Bussi for code review and feedback.

Edited clarified some points, cleaned-up, post still needs a re-structure

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