Re: [AMBER] cpptraj - RMSD

From: David A Case <>
Date: Sun, 9 Aug 2015 08:02:44 -0400

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?


> 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 ?


> 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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Received on Sun Aug 09 2015 - 05:30:02 PDT
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