[gmx-users] gmx check precision

jt555 jt555 at protonmail.com
Fri Mar 30 13:30:03 CEST 2018

Hello there,

I am currently using GROMACS version 5.1.2 and had a question in relation to the gmx check command. The following appears on the screen after invocation of gmx check -f protein.pdb:

GROMACS:      gmx check, VERSION 5.1.2
Executable:   /usr/bin/gmx
Data prefix:  /usr
Command line:
  gmx check -f protein.pdb

Checking file protein.pdb
Reading frame       0 time    0.000
# Atoms  9190
Precision 0.0001 (nm)
'GROtesk MACabre and Sinister t=  40.00000', 9190 atoms
Reading frame    6000 time 240000.000

Item        #frames Timestep (ps)
Step          6250    40
Time          6250    40
Lambda           0
Coords        6250    40
Velocities       0
Forces           0
Box              0

The precision = 0.001 nm, all my attempts at locating the answer for my questions proved futile.
Question) Invocation of similar command for XTC file (i.e., gmx check -f protein.xtc) also results in precision of 0.001 nm. However, in the manual it clearly states that .xtc exhibits greater precision in comparison to .pdb. If that is the case, then why am I observing the same value for precision in both? Or is it the case that because the system under investigation only contains 9,190 atoms, therefore the difference in precision between .xtc and .pdb is almost negligible and only realised when a much larger system is under investigation? FInally, could you kindly summarise the significance of precision obtained from gmx check command for a beginner?

I thank you in advance for your kind assistance.

Yours faithfully,


Sent with [ProtonMail](https://protonmail.com) Secure Email.

More information about the gromacs.org_gmx-users mailing list