[gmx-users] unexpecter rmsd

[Emran Heshmati]

Thank you Justin

On Fri, Mar 27, 2020, 19:47 Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/27/20 11:10 AM, Emran Heshmati wrote:
> > Thanks to Paul and jorden, I repost my question:
> > I am working on a protein consisting 2 chains. After performing
> > regular MD simulation
> > and analysis the outputs, I got unexpecter rmsd, as seen in link below.
> > What is the problem??
> > https://www.4shared.com/photo/cYHAiZgJea/New_Doc_2020-03-27_042856.html
>
> This is a PBC effect, with one or more protein chains jumping across a
> periodic boundary. Recenter with trjconv. You may have to center on one
> of the chains individually to get proper wrapping of the unit cell.
>
> -Justin
>
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