[gmx-developers] Velocity and force trajectory restricted to a group

David van der Spoel spoel at xray.bmc.uu.se
Tue Oct 9 22:42:59 CEST 2018

Den 2018-10-09 kl. 18:01, skrev Berk Hess:
> Hi,
> We don't have such functionality planned.
> But velocities are extremely correlated over several time steps. You 
> should be able to write output every 10 steps without significantly 
> reducing the statistics.
Depends what one is trying to sample of course. If hydrogen vibrations 
are being sampled both short saving times and decent precision are 
needed. However with a time step of 2 fs there likely are no hydrogen 

> Alternatively, if you are running in without domain decomposition, you 
> can quickly hack a printf statement in the code.
> Cheers,
> Berk
> On Oct 9, 2018 17:48, Andreas Baer <andreas.baer at fau.de> wrote:
>     Dear developers,
>     within my simulations, I encounter the problem, that I have to save
>     the forces and velocities of the whole system, even though I need
>     only those for very few atoms (in my case: a small particle e.g. a
>     fullerene, further details: see below). This generates a lot of
>     unnecessary data and also slows down the simulation a lot, as I have
>     to write out the trajectory every step (2 fs).
>     A possible solution would be to write forces and velocities only for
>     a group of atoms, as is possible for the compressed trajectory for
>     positions (.xtc). So far, I did not find any possibility doing that
>     and also no upcoming features.
>     Did I miss anything? If no, is this, or a similar functionality
>     planned for a future release?
>     If neither of this, is there a chance to do it myself, ether only
>     for my personnel use or as an official contribution?
>     Kind regards,
>     Andreas Baer
>     Some further details to my simulation:
>     A nanosized particle (artificial or fullerene) is dissolved in a box
>     of solvent (10^^5 to 10^^6 molecules). Transport coefficients should
>     be calculated using the Green-Kubo formalism. Thus, velocities and
>     forces are required at a very high frequency, so that I write out
>     every step. As I only need the information for the particle, I get a
>     huge amount of unused data, that I have to postprocess, to retrieve
>     the desired information. The biggest problem is, that this slows
>     down my simulation by a factor of roughly 20, depending on the
>     hardware used.

David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.

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