it depends on settings in your mdin file, what was your setting for iwrap?
On Thu, Jan 7, 2021 at 6:26 PM K Jan <10dunajkr.gmail.com> wrote:
> I will give that a go but in the amber tutorial it says: "in early
> versions of AMBER it was often necessary to re-image molecules back into
> the primary box before calculating RMSd fits. This is no longer necessary
> since by default AMBER tracks the original molecule, even if it moves out
> of the central box during the course of the simulation " so it shouldn`t be
> an issue.
>
> On Thu, 7 Jan 2021 at 22:45, Kenneth Huang <kennethneltharion.gmail.com>
> wrote:
>
> > Hi,
> >
> > Have you tried imaging/centering the molecule to make sure it's not an
> > effect of that? Ie, if you had a single protein residue in a water box
> >
> > parm *.prmtop
> > trajin run.nc 1 last 1
> > strip :WAT
> > center origin :1
> > image origin center familiar
> > rms first :1.CA,C,N,O
> >
> > I don't think the RMS fit alone would take care of the imaging/centering
> > hence why you get the huge spike, but someone who knows more might have
> > insight on that.
> >
> > Best,
> >
> > Kenneth
> >
> > On Thu, Jan 7, 2021 at 5:35 PM K Jan <10dunajkr.gmail.com> wrote:
> >
> > > Hi Amber users,
> > >
> > > I`m trying to calculate the RMSD of a 90 ps simulation of a molecule
> with
> > > cpptraj.
> > >
> > > The rmsd increases from 0 to 17 Angstroms in the 90 ps which is clearly
> > too
> > > big. I`ve also checked the vmd and my molecule is translating around
> the
> > > screen a small amount and vibrating a little, but the structure of it
> > > doesn't change at all, which is strange because the radius of gyration
> > has
> > > increased, which should mean that the compactness of my molecule has
> > > decreased but that hasn`t happened.
> > >
> > > I read that I have to perform a least-squares fit to remove the global
> > > rotation and translation. I am not sure how to do this and would
> > appreciate
> > > some advice. I read that I could do this on the vmd by using the rmsd
> > > trajectory tool but when I try and press align in the tool it says that
> > no
> > > atoms have been selected, even though I wrote protein in the atom
> > selection
> > > box, and I have loaded up the topology of my molecule and the
> trajectory
> > > files from my simulation.
> > >
> > > Would appreciate some help.
> > >
> > > Thanks ,
> > > Kris
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> >
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> imprisoned
> > here could not dream of heaven?
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Received on Thu Jan 07 2021 - 18:00:02 PST
