Re: [gmx-users] how to optimize the orientation of the protein in a dodecahedron

Hi Thomas, Apologies, you are right. I was thinking of the distance to the wall. If the protein is elongated, it will matter in the minimal distance whether the protein major radius is oriented towards a face or towards a corner. In addition, the shape of the protein plays a role. Yet it doesn't r

Re: [gmx-users] how to optimize the orientation of the protein in a dodecahedron

Hi Tsjerk and Erik, Thanks for the comments. It's strange, because I get different minimum distance for different orientations of the same protein structure using the afore-mentioned command lines. I used a single step energy minimization for speed (em_real.mdp). Below are the outputs of editconf

Re: [gmx-users] how to optimize the orientation of the protein in a dodecahedron

Hi, And even if not all orientations are exactly equal in this respect, bare in mind that the solute might rotate during the simulation, taking it out of any optimum. Erik 26 apr 2012 kl. 14.36 skrev Tsjerk Wassenaar: > Hey Thomas, > > The rhombic dodecahedron corresponds to the packing of a

Re: [gmx-users] how to optimize the orientation of the protein in a dodecahedron

Hey Thomas, The rhombic dodecahedron corresponds to the packing of a sphere. Consequently, the difference in the distance between periodic images over the shortest diameter and the longest diameter is pretty small. That means that there isn't really an optimal orientation in a rhombic dodecahedron

[gmx-users] how to optimize the orientation of the protein in a dodecahedron

Dear GROMACS users, I have noticed that for constant box dimensions the minimum distance from the periodic images of a protein depends on the initial orientation of the protein, whereas the orientation of the dodecahedron relative to the x,y,z axes remains fixed. These are the command lines I use: