GROMACS version:
GROMACS modification: No
Good afternoon.
My name is Paula Antelo and I am student at the University of Santiago de Compostela. I have been using MDAnalysis, in order to analize molecular dynamics simulations, until I found the following inconvenient.
When realizing the mentioned simulations I use gromacs and obtain two different file types to work with: file.xtc and file.gro. The resolution that coordinates are saved with on the file.xtc is specified by myself when executing the simulation using gromacs (compressed-x-precission parameter in the file.mdp), that means that the number of decimals coordinates are saved with is completely determined. This in important to understand the problem I am about to introduce.
A universe is created using MDAnalysis, involving the file.xtc and the file.gro. The following step is to select atoms and to read their coordinates, for which I call the function Atom.position. When printing coordinates with a considerable number of decimals (exactly thirty in my sample) it may be observed that the number of decimals does not correspond with the one I had specified before when executing the simulation with gromacs. Here is an example of this: if I indicate that I want two decimals then I observe that two decimals are printed, followed by three ‘0’ values, but the following decimals are not zero, although they should according with what I had specified.
The important issue appears when a higher resolution is required, for example five decimals, since in that case I can not distinct any more what decimals are actually my atoms coordinates and which ones are added by Python or MDAnalysis.
For a clearer explanation an image is attached at the end of this email, where four examples of printed coordinates are illustrated, specifying the previously indicated resolution for their generation.
I would honestly feel thankful if a solution for this was reached, since it is important for my current work.
Thank you beforehand.