Hi,
Can you please state what version of CPPTRAJ you are using, and your
complete CPPTRAJ input? Thanks,
-Dan
On Wed, Mar 18, 2026 at 8:56 AM Ivana Nikšić-Franjić via AMBER <
amber.ambermd.org> wrote:
> Dear Sir or Madam,
>
> I am trying to extract hydrogen bonds within the first and second
> hydration shells around the tetraphenylborate anion. I have used the
> following cpptraj commands: radial, watershell, closest, and hbond. From
> the RDF curve, I identified the first minima at 6.5 and 9.6 Å. When
> using the solute center option, the distances are calculated from the
> geometric center.
>
> However, in subsequent steps with the watershell and closest commands,
> it appears that distances are not measured from the geometric center or
> center of mass. Instead, they seem to follow a nearest-solute-atom
> approach. As a result, when I visualize the selected water molecules,
> they appear at significantly larger distances when measured from the
> center (e.g., the boron atom).
>
> Is it possible to configure the watershell and closest commands to use
> the center of mass instead? If so, how can this be achieved?
>
> Thank you in advance for your help.
>
> Best regards,
> Ivana Nikšić-Franjić.
> --
> Ivana Nikšić-Franjić
> Institut Ruđer Bošković$Bijenička cesta 54
> <https://www.google.com/maps/search/Bijeni%C4%8Dka+cesta+54?entry=gmail&source=g>$10000
> Zagreb$Croatia
>
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Received on Thu Mar 19 2026 - 03:30:02 PDT
