What kind of restraints did you use, and how strong? How high is the
penalty energy in the mdout file?
On Tue, Sep 17, 2019, 5:15 AM Amit Kumar <ak543714.gmail.com> wrote:
> I am really very sorry sir, I miswrote the question.
> I found the RMSD value of the restrained system higher than the
> unrestrained system, which is very unusual. I am also attaching the
> result.
>
> On Mon, Sep 16, 2019 at 6:57 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > Yes this is very sensible. I would expect that the restraints would keep
> > the structure closer to the initial model (if that's what you use as the
> > reference for rmsd), leading to lower rmsd with the restrained
> trajectory.
> >
> > On Mon, Sep 16, 2019, 9:20 AM Amit Kumar <ak543714.gmail.com> wrote:
> >
> > > Dear Amber users,
> > > I ran a simulation of a fibrillar protein for few nanosecond (with and
> > > without torsional restraint) using Amber16. I used implicit solvent
> > (igb=5)
> > > results when analysed in terms of RMSD, the RMSD value of the
> > unrestrained
> > > system was higher than the RMSD value of the restrained system. Is it
> > > possible? Can you explain the phenomenon?
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Received on Tue Sep 17 2019 - 04:00:02 PDT
