[gmx-users] Calculating the distance between protein and ligand during ligand diffusion out of the box

bipin singh bipinelmat at gmail.com
Mon Oct 7 16:46:30 CEST 2013

Hello All,

I have calculated the distance between the binding pocket of protein and
the ligand molecule but due to ligand diffusion out of box, I am getting
wrong distance as first it increases till 5nm and then decrease again to
around 1nm during the simulation (which is not possible).

I have fitted my trajectory with using trjconv -pbc mol -ur compact -center
(protein) option.

I have also tried the -nojump option but getting the same results for

Please suggest how to get the real distance without the PBC effect.

Thanks and Regards,
Bipin Singh*

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