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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Aug 09 2015 - 14:00:03 PDT
