[gmx-users] Position Restraints problem

[Mark Abraham]

Hi,

Sounds completely normal. Please see
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Mark

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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