Distance between COM HP-beta-cyclodextrin and Gliclazide

User discussions
1

Hi everyone,

I’m trying to calculate the distance between the center of mass (COM) of HP-beta-cyclodextrin and gliclazide during a simulation using gmx distance, as referenced in this paper, However, I keep getting the following error:

Inconsistency in user input:
Selection ‘GLZ’ does not evaluate into an even number of positions (there are 43 positions)

Gliclazide consists of 43 atoms, so I assume this error is due to GROMACS expecting an even number of positions for the selection.

How can I properly define the selection so that gmx distance calculates the COM distance correctly? Is there a way to force GROMACS to compute the COM even with an odd number of atoms, or should I modify the selection somehow?

Any help would be greatly appreciated!

Thanks in advance.

2

Hi,
As far as I understand you want to calculate the distance between two or more selections. In that case gmx pairdist is better

To have the com of molecule, you could define the molecule in your index file and use option like -selrpos

Here you find a brief description for the difference between gmx distance gmx pairdist

I hope it helps
Alessandra
Here you find more on Topics tagged gmx-distance

3

I see, thank you so much for the response!!