[gmx-users] g_dist tools

[Mark Abraham]

Hi,

We can't tell what you want to do, so perhaps you should read the help for
gmx distance and choose accordingly.

Mark

On Thu, Jun 4, 2015 at 9:13 PM Poncho Arvayo Zatarain <
poncho_8629 at hotmail.com> wrote:

> Hello, i want to run this command: echo "3 4"| g_dist -f
> dppc128_1-nj-ct-nobox.xtc -
> s dppc128_1.tpr -o dppc128-Dpp.xvg -n Dpp.ndx -b 20000 in Gromacs 5.0.4
> but when i run it, the following appears: This tool has been removed.
> Please see tool changes for 5.0. And when i see th tools appears:
> g_dist: This tool has been removed in 5.0. A replacement is gmx distance
> (for most options) or gmx select (for -dist or -lt).If you had index groups
> A and B in index.ndx for g_dist, you can use the following command to
> compute the same distance with gmx distance:gmx distance -n index.ndx
> -select 'com of group "A" plus com of group "B"' -oxyz -oall
> The -intra switch is replaced with -nopbc.
>
>
> If you used -dist D, you can do the same calculation with gmx select:
>
> gmx select -n index.ndx -select 'group "B" and within D of com of group
> "A"' -on/-oi/-os/-olt
> You can select the output option that best suits your post-processing
> needs (-olt is a replacement for g_dist -dist -lt)
>
>
> Shoukd i use -dist or -intra option?
>
>
>
>
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