[gmx-users] Position Restraints problem

Mark Abraham mark.j.abraham at gmail.com
Wed Oct 14 20:42:17 CEST 2015


Sounds completely normal. Please see


On Wed, Oct 14, 2015 at 3:08 PM Chiara Bello <kiarabell at msn.com> wrote:

> Hi, I'm trying to apply the positions restraints only on alpha helices of
> my protein but after running mdrun, when I open the output pdb file using
> vmd, the protein appear broken: there are some atoms of the not restrained
> residues, that have been separated from the protein.
> My simulation is in implicit solvent, I have used Charm27 and
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