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

Andreas Baer andreas.baer at fau.de
Tue Oct 9 17:48:05 CEST 2018

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.
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