[gmx-users] Question

Mark Abraham mark.j.abraham at gmail.com
Wed Aug 12 22:38:43 CEST 2015


On Wed, Aug 12, 2015 at 9:47 PM Eric Smoll <ericsmoll at gmail.com> wrote:

> 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.

That's not an operation that mdrun supports. You can get all the
coordinates and velocities, or a subset of the coordinates at a user-chosen
precision, but that's all.

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.

This is a limitation of the current GPU implementation - energygrps is not
supported (and your md.log file will say this).

Is there someway I can request that gromacs only compute the
> energy of one group in my system?

Only when you postprocess the trajectory on just the CPU, e.g. with mdrun
-rerun traj -nb cpu

Will this result in a speedup?

No. The bulk of the work is in the forces, so any savings from the energy
calculation on only part of the interactions would be offset by the need to
run a separate GPU kernel and do more book-keeping, so probably no gain.
But as above, none of this is implemented.

> 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?

Speedup on a single GPU with a comparable CPU, yes.


> Best,
> Eric
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