[gmx-users] gmx trjconv trr xtc

Mark Abraham mark.j.abraham at gmail.com
Wed Mar 13 09:47:00 CET 2019


XTC is a reduced-precision format for coordinates. This is fine for most
use cases, because the difference between 2.012 nm and 2.013nm is dwarfed
by the other modelling approximations (fixed point charges! short
sampling!). It gives you the advantage of using less disk and spending less
time handling files. Further, it leverages the knowledge that in e.g. a
water molecule, the three atoms are not in arbitrary locations, but can be
stored efficiently as a position and two deltas. See


On Tue, 12 Mar 2019 at 00:57 Alex <alexanderwien2k at gmail.com> wrote:

> Dear groamcs user,
> A system of mine contains two molecule type of A and B in water. Using
> gmx trjconv -f out.xtc -o out.last.5ns.trr I  first truncated the last 5ns
> of the system's XTC file as a TRR file and just selected the non-water
> contents so that the TRR file only has A and B. The TRR file is 4.4 GB.
> Then I applied again the "gmx trjconv -pbc cluster -center yes -f
> out.last.5ns.trr -o out.last.5ns.xtc" and again just non-water was chosen.
> I was expecting that the both out.last.5ns.trr and out.last.5ns.xtc would
> have the same size 4.4 GB as the material in both of them are just A and B,
> however, the out.last.5ns.xtc is just 1.4 GB!
> I wonder if that is normal? here I just care about the coordinates
> dynamically and not velocity, do you think I am loosing any coordinate in
> by the second command from out.last.5ns.trr to out.last.5ns.xtc?
> Regards
> Alex
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