Re: [AMBER] distance restrain

From: Jason Swails <>
Date: Fri, 12 Jun 2015 05:24:44 -0400

On Thu, Jun 11, 2015 at 4:11 PM, Lara rajam <> wrote:

> Dear Amber ,
> I am trying to do the Distance restrain simulation .
> I have fixed two atoms with their atom number and I would like to decrease
> the
> distance between these two .
> could anyone suggest me how to do this .,
> I have read the manual that the DISANG file the r1 , r2 , r3 , r4 values
> should be given in increasing order ., how to do this if i want to decrease
> it.

​r1, r2, r3, and r4 are simply 4 points defining the different sections of
a flat-well potential. For a harmonic potential, r2 == r3 and r1 << r2 and
r4 >> r3. But r2/r3 is the center of the harmonic potential.

Do you want to gradually decrease the distance between the two atoms over
the course of the simulation? In that case, you should look at the "jar"
keyword and the description of steered MD in the Amber 15 manual.

Or do you just want to make the restraint distance smaller without changing
it during the simulation? In that case, just make r2 and r3 smaller...
 (and adjust r1 and r4 accordingly if necessary).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Jun 12 2015 - 02:30:03 PDT
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