ericsmoll at gmail.com
Wed Aug 12 23:12:03 CEST 2015
Mark and Justin,
Thank you for the help. It is much appreciated.
Is there a way to prevent the output of an .edr file altogether? Is there a
way to prevent the output of a .trr file all together?
On Wed, Aug 12, 2015 at 2:38 PM, Mark Abraham <mark.j.abraham at gmail.com>
> 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
> > 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
> > 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
> > have 20,000-40,000 atoms with PME and 1.5 nm cutoffs. Are these
> > well suited for GPU acceleration or is this unlikely to produce a
> Speedup on a single GPU with a comparable CPU, yes.
> > Best,
> > Eric
> > --
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