[gmx-users] gmx trjorder

[Christian Blau]

Hello Akash,


Not knowing much more about your this system, this looks reasonable to me and should give you the count you just described.


Best,

Christian

On 11/7/19 2:44 PM, Pandya, Akash wrote:
> Hi,
>
> I would like to calculate the number of ligand molecules within 0.5 nm of a particular amino acid in my protein. I came across the gmx trjorder command (as shown below).
>
>
> gmx trjorder -f Traj.gro -s Traj.tpr -n ProteinLIG.ndx -nshell nshell1.xvg -b 20000 -e 40000 -na 10 -r 0.5
>
>
> I have 10 atoms in my ligand. I wanted to ask how accurate is this command in trying to calculate what I want?
>
>
> Akash
>