[gmx-users] gmx trjconv trr xtc

Dallas Warren dallas.warren at monash.edu
Tue Mar 12 03:22:51 CET 2019

.trr and .xtc are two different file formats, with the latter being
compressed.  Therefore, an .xtc file will be significantly smaller than a

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a

On Tue, 12 Mar 2019 at 10:56, 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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