Hello Stephan,
I add nofit and it worked.
Thank you,
Hadi
On Tue, Sep 4, 2018 at 4:58 PM Stephan Schott <schottve.hhu.de> wrote:
> Hi Hadi,
> The issue is that rms by default makes a best rms fit. To avoid this, add
> nofit to your command. Also, if you want to make an rms fit to a reference,
> you have to specify this instead of first. You can check the options of
> different commands with " help <command> ".
> Hope it helps,
>
> El mar., 4 sept. 2018 a las 22:36, Hadi Rahmaninejad (<
> ha.rahmaani.gmail.com>)
> escribió:
>
> > Hello Ambe Users,
> >
> > I am calculating rms of a single atom (Methane) in a system. There are
> some
> > atoms which I made them fix using "ibelly", but not the methane. When I
> > visualize methane with vmd it is clearly moving. However, when I am
> > calculating the rms using cpptraj program, the output is zero. the
> command
> > for cpptraj which I used is like below:
> > trajin 03_equil.nc
> > reference 02_Heat.rst
> > rms first out 03.rms :4201.ME
> >
> > I highly appreciate if you have any suggestion.
> > Thank you in advance,
> > Hadi
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Stephan Schott Verdugo
> Biochemist
>
> Heinrich-Heine-Universitaet Duesseldorf
> Institut fuer Pharm. und Med. Chemie
> Universitaetsstr. 1
> 40225 Duesseldorf
> Germany
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Received on Tue Sep 04 2018 - 14:30:02 PDT
