I’m currently working on developing methods that accelerate sampling in molecular dynamics simulations proteins and other biomolecules. At biological temperatures, for many such systems there is a large gap between the time step used to integrate the equations of motion (in the order of femtoseconds) and the times characteristic of the functional motions we are interested in studying (milliseconds). This makes relevant time and length scales infeasible to probe with conventional simulation techniques and limited computing resources. With the help of higher sampling efficiency however, we can explore longer physical time and length scales in a reasonable computing time.
I am currently working on an developing the acceleration weight histogram method (AWH) and applying the method to biological systems. I keep an open code branch of AWH built on GROMACS available at Bitbucket. Feel free to try it out: bitbucket.org:vivecalindahl/awh-gromacs-open.git
To see my publications, visit me at Google scholar . It should be up to date. Also, have a look at my
- poster from “Workshop on free energy methods in drug design”, Boston 2014
- poster and talk from EBSA 2015 European Biophysics Congress