[gmx-developers] Coming on to help in GROMACS development
mrshirts at gmail.com
Wed Mar 9 20:05:24 CET 2005
My name is Michael Shirts, and I'll be starting to do some development
work on GROMACS in consulation with Erik Lindahal. I'm currently and
I'm a new postdoc in Rich Friesner's group at Columbia. I recently
graduated from Stanford, where I was in Vijay Pande's group, working
on Folding at Home (http://folding.stanford.edu), and worked closely with
Erik Lindahl, then a postdoc in Michael Levitt's group at Stanford, to
help implement features in GROMACS that we required in our work. My
CV is at http://www.columbia.edu/~mrs2144/MRSCV.html -- my work with
GROMACS is almost entirely in the three papers in press or just
submitted, so you'll have to wait a little bit for that :)
I've done some work on the GROMACS code itself already -- I rewrote
the routine for the mean field dispersion correction to the
Lennard-Jones cutoff, adding the effect of the switching or shifting
function, as well as a few other bug fixes.
Based on my previous research, I've got a few other things that I'll
be working on that I'd like to put into the next couple releases of
GROMACS. Please comment on any of these features that you find
interesting (or think that really don't need to be implemented, etc).
1) Improved free energy features, including
a) decoupling free energies capabilities (there are
problems with decoupling energies with Coluomb in
b) output suitible for after the fact FEP and Bennett
acceptance ratio computations, over multiple states
c) an improved, more comprehensive tutorial for free
d) including forces from restraints in free energy
2) Velocity Verlet integrator as an option:
This is important for pressure control calculations, as
the calculation of the box size at time t+dt requires the
pressure at time t, which in turn requires both the virial
and the velocities at t, which is not possible with leapfrog
Verlet -- approximations are necessary.
3) Adding bookkeeping so that if there is a conserved
quantity in the simulation (energy, or enthalpy, or
whatever), it will be kept track of separately, in order to
help judge the goodness of fit.
4) Improved pressure control, adding Andersen pressure
control as well as Parinello-Rahman, and fixing some bugs
in the current P-R implementation.
5) Andersen temperature control, which is a useful
alternative to Nose-Hoover when there are highly
decoupled degrees of freedom, and equipartion is
Thanks for your input, and I look forward to working with all of you!
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