[gmx-users] inconsistent shifts while using distance restraints

Kortzak, Daniel d.kortzak at fz-juelich.de
Thu Apr 7 15:08:11 CEST 2016

Dear gmx-useres,

I am simulating a protein in a box with water and ions and now I am trying to keep the ions away from a particular residue of the protein. To do this I am using distance restraints. So I created a new molecule type with the protein and all ions and added distance restraints between each ion and the C-alpha of the residue in the protein. To get a repulsive flat-bottom distance restraint I set low to 0.9 nm and up1,up2 to 98, 99nm (box vectors are all around 15nm).
Everything seems to be working fine (in some 3000steps test simulations) but mdrun prints the message "There were inconsistent shifts." I guess this is because I have distance restraints between atoms that are further away from each other than half the shortest box vector, but since there is no force acting on those pairs I would not worry too much. So my questions are:
Is my guess correct?
Is there a better way than distance restraints too keep the ions away from their binding site?
Here I have to add that the protein is actually a dimer so I have two distance restraints per ion, that is the reason to choose distance restraints rather than position restraints.

Daniel Kortzak

Forschungszentrum Juelich GmbH
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Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt

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