[gmx-users] Regarding high RMSD

[Alessandra Villa]

Hi,
I suggest to visualize your trajectory. Maybe one of the peptide is
diffusing away from the other.
Or the one peptide is jumping in and out or moving out the box.
If it is the case, here you found some trjconv workflow
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Best regards
Alessandra


On Wed, Jan 15, 2020 at 11:21 AM Ashma Khan <ashmakhan200 at gmail.com> wrote:

> Dear all,
> I have calculated the c-alpha RMSD of dimer having 7 residues peptide each
> by using command gmx rms. But the calculated RMSD 14 Angstorm is very high,
> although I have applied all pbc conditions. Anybody can suggest me why so
> much high RMSD is coming or is it possible.
>
> --
> Ashma Khan
> Research Scholar
> Department of Chemistry
> AMU, Aligarh
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