Yes, just download AmberTools 15 for free: http://ambermd.org/#AmberTools
Hai
On Sun, Aug 9, 2015 at 4:50 PM, Amber mail <amber.auc14.gmail.com> wrote:
> Dear dac,
>
> Thanks a lot for your help!
>
> Is it possible to upgrade ambertools 12 to ambertools 15 freely, or should
> I get the full Amber 15 package ?!
>
> Best Regards,
> Alaa
> On Aug 9, 2015 3:03 PM, "David A Case" <david.case.rutgers.edu> wrote:
>
> > On Sun, Aug 09, 2015, Amber mail wrote:
> >
> > > > rms reference mass out 02_03.rms time 10 :44-61
> > > >
> > > 1- Does the " time 10 " indicate the time of each frame in ps ?
> >
> > It tells cpptraj the time between snapshots, in whatever units you wish.
> > (ps or ns are common units). This is only used to replace the frame
> number
> > with the elapsed time in writing some output files.
> > >
> > > This how I calculated the value of 10
> > >
> > > No. of frames = nstlim/ ntpr =5000000/5000=1000 frame
> >
> > You should use ntwx, not ntpr, here. In your example, they are both the
> > same.
> >
> > >
> > > Simulation time =nstlim*dt = 5000000*0.002=10000 ps
> > >
> > > Time of each frame = simulation time/no.frames= 10 ps
> >
> > Works. But simpler is just ntwx*dt.
> > >
> > > 2- Does " :44-61 " mean to specify residues from 44-61 only?
> >
> > Yes.
> >
> > >
> > > Should I also add the command " strip: WAT " to exclude all water
> > molecules
> > > from RMSD ?
> >
> > You don't need this, unless some of the residues 44-61 are in fact water
> > molecules. (But in that case, you should just change ":44-61" to what
> you
> > really want.)
> >
> > > So does this graph represent the time of MD simulation in (ps) on
> x-axis
> > > and the RMSD in (Angstroms) on y-axis ?
> >
> > Yes.
> >
> > >
> > > I just want to double check my work because I am not sure that I well
> > > understand the part concerned with cpptraj in AmberTools12 Manual
> >
> > I strongly urge you to upgrade to AmberTools15. cpptraj is being
> developed
> > now at a very rapid pace. Simple tools like "rms" are probably fine in
> the
> > older version, but many bugs have been fixed and new feature added. Even
> > the manual is better (although still far from perfect.)
> >
> > ....good luck....dac
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Sun Aug 09 2015 - 14:30:02 PDT
