Teresa Paramo

Hi again David ;) The index you should use is Protein, because this is the group of atoms you want to find cavities in, right? Apparently the program is not finding cavities between the solvent atoms, and therefore there is just a sphere in the 0,0,0 coordinate because it is initialised there when nothing is found. I think you should use a dimension 6 or 5 instead... also a 1.4 angstrom spacing it is usually fine (approx. radius of a water molecule). Good luck! On Sun, 24 Jan 2021 at 21:20, David...

Hi David, I feel that this should not be an issue with either gro or xtc files (a different thing would be the tpr file), but I can’t confirm... check that out and let us know! :) Cheers On Sun, 24 Jan 2021 at 19:38, David Huebert davidhuebert@users.sourceforge.net wrote: Dear Teresa, Thank you very much. I read this and a previous post in another discussion to place Gromacs 5.1.4 with Trj_Cavity-2.0.3. My only question is if I submit files .gro and .xtc files from a Gromacs-2020.2 run into the Gromacs5.1.4+Trj_Cavity-2.0.3...

Hi David, As stated in the home page: trj_cavity v2 runs in parallel and supports GROMACS v5.1+ series. If you want to continue on using GROMACS v4.x, please use trj_cavity_v1.1. As I have recollected from other discussions, versions after the 5.x series changed the API once again so previous third party applications such as trj_cavity v2 are not compatible (v2 was already refactored from v1 to be compatible with those versions). In summary, v1 goes with gromacs4 and v2 with gromacs 5.1+. Hope this...

Hello Anna, It is the standard deviation. All the best

Uff, I am glad! Have fun :)

I would not work - according to the license of gromacs, the library needs to be remain external because they forbid its distribution, and you are having problems with gromacs. In this thread, somebody had the same issue as you with gromacs 5.1.4, and made it work... https://sourceforge.net/p/trjcavity/discussion/general/thread/312ce4ae/ So the sources are ok, the problem lays in your system. Some other users had problems because they were mixing compilers - that is, they compiled gromacs and trj_cavity...

Sorry, I meant newer - one with that problem solved.

Well, so we have reached an impass here. trj_cavity works under the gnu compiler collection but boost is c11 and it seems that they won´t co-exist. If you manage to run without declaring that libary on the makefile, cool. Otherwise go for an older gromacs version, because it seems that this one does not have their analysis suite well configured.