[gmx-users] Regarding high RMSD

[Alessandra Villa]

Hi,

On Fri, Jan 17, 2020 at 6:39 AM Ashma Khan <ashmakhan200 at gmail.com> wrote:

> Thank you for your suggestion Alessandra Villa
> I have applied all types of pbc conditions but my one peptide is diffusing
> away from another peptide in case of dimer after half of the simulation
> time and rmsd is coming out 100 Angstrom after that time which is very
> high. Please suggest me what should I do.
>

When you visualize the trajectory (for example in VMD), you see the dimer
breaking and the two peptides moving apart inside the box
(in a "continuous" way and not jumping in and out the box or moving out of
the box).
That probably means that in your simulation condition, the two peptides do
not form a dimer.

Best regards
Alessandra





> --
> Ashma Khan
> Research Scholar
> Department of Chemistry
> AMU, Aligarh
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