[gmx-users] Using higher precision with gmx distance and analyze

Mark Abraham mark.j.abraham at gmail.com
Wed Mar 22 22:49:56 CET 2017


On Wed, Mar 22, 2017 at 9:17 PM Irem Altan <irem.altan at duke.edu> wrote:

> Hi,
> I have some .gro files I generate from trajectories using the -ndec flag
> to print positions with higher precision (specifically, -ndec 14).

You don't create any more precision than is in the original trajectory
files, so unless you need these gro files for something else, you may as
well use the original ones (saving time and disk space).

> I subsequently analyze these .gro files using gmx distance and gmx
> analyze. There doesn’t seem to be a similar -ndec flag for these commands,
> however.

Yes, as you can see in gmx help trjconv, -ndec controls precision of output
trajectory formats. It doesn't affect .xvg output.

> The .xvg files are printed out such that I get 3 digits after the decimal
> for distances in nanometer. Is there any way I can use these commands that
> carry out analyses with the same higher precision?

No, the tools work in the full precision of however they were compiled
based on whatever data they read in, and the output from that has precision
that is hard-coded in the individual tools. But it is doubtful that even
0.001 nm of coordinate precision is meaningful, given the limitations of a
typical model physics.


> Best,
> Irem
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