[gmx-users] Question

Eric Smoll ericsmoll at gmail.com
Wed Aug 12 21:47:27 CEST 2015

Hello gromacs users,

I am running a set of MD simulations where we are only interested in
logging the coordinates and kinetic energy of a specific group in the
system. I want to write the coordinates and energy of this group to file at
every timestep.

Supplying an index file with the group of interest to grompp and specifying
this group in the mdp file under "energygrps" doesn't seem to impact the
edr file. The edr file still outputs the total system energy as a function
of time. Is there someway I can request that gromacs only compute the
energy of one group in my system? Will this result in a speedup?

Are there other ways I can increase the speed of my simulation? My systems
have 20,000-40,000 atoms with PME and 1.5 nm cutoffs. Are these simulations
well suited for GPU acceleration or is this unlikely to produce a speedup?


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