[gmx-users] calculate *all* carbon atom distances over time?

[Athina Meletiou]

Hello all,

I was wondering how I could measure the distance over time between all my carbon atoms in my simulation. My molecules have interesting folding patterns and I would like to see the distances between the unconnected carbon atoms as my molecules fold and unfold through the simulation. My simulations consist of single lipid molecules in water.

I have tried using g_dist but it seems that it's not what I'm looking for as it calculates distances between groups of atoms rather than individual atoms. Do you think that gmx distance (Gromacs 5.0) will help me? What concerns me is that in the gmx distance reference it states that "gmx distance calculates distances between pairs of positions as a function of time" - do the positions need to be in pairs, as in always in even numbers?

Thank you all very much,

Athina




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