[gmx-users] wandering

Nagy, Peter I. PNAGY at UTNet.UToledo.Edu
Wed Jul 9 23:38:01 CEST 2003

Dear Gromacs Users!

    I think, this problem has emerged many times, so please direct me if there are answers somewhere.

    I performed a 10 ps test run for a protein consisting of 26 residues and about 600 water molecules. Everything went seemingly properly. When I looked at the protein dynamics using ngmx I found that the protein was much out of the box. I assume that a translational motion was allowed although the center of mass should not move, and originally the software places the protein within the box, I presume. There must be periodic boundary conditions, so the protein would remain solvated even leaving the box, yet I am worried about the translation.

    The question is: how could I keep the solute strictly within the box, thus 
preventing translation?

Thanks, Peter Nagy

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