[gmx-users] centroid distance for tyrosine

[Archana Sonawani-Jagtap]

Hi Justin,

I think something is wrong in the command because when I visualize the
distance between OH atoms of tyrosine's in VMD it shows ranging from 3 to
10 ang. Also, when I take single frame in pdb format and check centroid
distance using PIC webserver, it gives within same range. However, using
above command it gives distance within 1.37-1.38 ang.

I used following command:

gmx distance -f apo-cxcr4-final1.xtc -s mdmodified_cxcr4.tpr -n
nter_index.ndx -oav distave_tyr12-21.xvg -select 12Y_cog  21Y_cog -oall
dist_tyr12-21.xvg

What could be wrong?





On Sat, Feb 16, 2019 at 4:31 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/15/19 2:37 PM, Archana Sonawani-Jagtap wrote:
> > Hi,
> >
> > I want to calculate centroid distance between 2 tyrosine rings throughout
> > the simulation. Which option of gmx distance can help to plot the
> centroid
> > distance?
>
> Create two index groups with the ring atoms, then use gmx distance:
>
> gmx distance -s -f -select 'cog of group "ring1" plus cog of group "ring2"'
>
> -Justin
>
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