[gmx-users] gmx check precision

Justin Lemkul jalemkul at vt.edu
Fri Mar 30 15:33:52 CEST 2018

On 3/30/18 7:29 AM, jt555 wrote:
> 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

Where does it say that?

> that is the case, then why am I observing the same value for precision in both? Or is it the case that because the

The default precision for an .xtc file is exactly what you're seeing, 
unless you're changing it in the .mdp file to save more decimal places.

> 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

The precision of output files is not related to the size of the systems.

> summarise the significance of precision obtained from gmx check command for a beginner?

It's just reporting how many decimal places are saved.


> I thank you in advance for your kind assistance.
> Yours faithfully,
> J.
> Sent with [ProtonMail](https://protonmail.com) Secure Email.


Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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