[gmx-users] gmx distance

[Sahil Lall]

Hello, 

Put both the indices in the same file as 

[ A ]

*atoms numbers of residue 130* 

[ B ] 

*atom numbers of residue 153* 

and save this file with a .ndx extension (e.g. dist.ndx). Now, provide
that file name with the -n option in gmx distance. Upon execution, it
will automatically ask you which index groups to use for distance
calculation where you can provide A and B as inputs. 

Cheers 

On 2019-12-19 14:39, Emran Heshmati wrote:

> Dear All
> I am in trouble with gmx distance command. I want to calculate the distance
> between two amino acids (residue 130 and residue 153) in a protein after
> gromacs standard simulation. After generating of r130.ndx and r153.ndx
> index files, I use this command:
> gmx distance -f md_0_1_noPBC.xtc -s md_0_1.tpr -oav distave.xvg -oall
> dist.xvg -oh disthist.xvg -b 70000 -e 100000
> but don't list r130 and r153 as extra groups. Adding -n *.ndx option
> didn't  sole the problem. Any comment please.