[gmx-users] gromacs with turbomole?

Hi, I am looking for viable systems for doing QM/MM calculations and as I have experience with both Turbomole and GROMACS I am wondering if there is anyone using these two together. I have found this ("The Quick and Dirty GROMACS-TURBOMOLE interface") at https://github.com/rmera/qdgt , but it

[gmx-users] g_rms using a structure in trajectory as reference

Hi, I am trying to understand how to best use a chose frame in the trajectory as reference structure for the analysis when using for instance g_rms or g_rmsf. For instance, if I want to see how the structure changes with respect to the structure 20 ns after the beginning of the simulation. If

Re: [gmx-users] Creating topology for Cu-containing enzyme,

Hi, Thank you Joao, Justin and Marlon for your answers. Joao, I have been looking at your article the last days as it explains very well what you have done, particularly in the Supplementary info, so I am very happy that you answered this thread. Would it be possible for me to look at your

[gmx-users] Creating topology for Cu-containing enzyme, GROMOS96 force field.

I am interested in a metalloenzyme with Cu and I have found several studies in the literature on systems similar to mine using GROMACS and the Gromos force field. I see that GROMOS contains parameters for Cu, and I intend to keep the Cu-protein distances for the ligand atoms fixated during MD