Re: [AMBER] Distance between two atoms vs time

From: Billy Miller III <>
Date: Mon, 22 Mar 2010 08:57:13 -0400

Once you trajin the correct trajectory file, the general command for
calculating the distance between two atoms should be something like this:

distance DIST .atom_number1 @atom_number2 out dist.out

Or for your specific case, it should be:

distance DIST .256 @399 out dist.out

You could also use the residues numbers and atom types:

distance DIST :154.OE1 :45.OD2

Either of these last two commands should give you the exact same results for
your system.

Good luck!

-Bill Miller

On Mon, Mar 22, 2010 at 8:24 AM, imtiaz shafiq <>wrote:

> Dear All,
> I want to calculate a distance between two atoms vs time. Let us say I
> have two atoms with number 256 and 399 and the corresponding residue
> names are GLU 154 and ASP 45, The atom label are OE1 and 0D2, what
> could be the best option to calculate distance between these two
> versus the time.
> I have look at the Amber tools manual and found there is distance
> command available with ptraj but I am not sure what syntax I should
> use in my case. Please suggest me something in this regards
> Imtiaz
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Received on Mon Mar 22 2010 - 06:00:10 PDT
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