Re: [gmx-users] g_mindist after trjconv -fit give different results

Hi Elad, You can't count on operations that involve PBC after fitting. In your case, you can use trjconv -fit translation to remove translational degrees of freedom only, keeping the system consistent with PBC. Hope it helps, Tsjerk On Sun, Dec 6, 2009 at 8:50 PM, el...@post.tau.ac.il

[gmx-users] g_mindist after trjconv -fit give different results

Hi Tsjerk, thanks for the reply. Will the MSD of the molecule also be affected by the fitting. I'm trying to calculate the relative diffusion coefficient of an ion near a protein. For this I thought to first fix the system according to the protein and then calculate the msd of the ion. I