Re: AMBER: Distance restraints between center of mass of two molecules

From: Sudha Mani Karra <>
Date: Wed, 15 Aug 2007 10:40:37 -0500

Hey Carlos,
       Thank you.
If you are familiar with the distance restraints, could you help me in
uderstanding the following?

The md input file is

   imin=0, irest=1, ntx=7,.......,
 &rst iat=1, 6, r1=0.0, r2=..., r3=..., r4=...,
In the above, for simple harmonic restraints we take r1=0.0 ,r2=r3 and r4 to
be a large value.
IF my R is say around 8 A then what should be the r2, r3 and r4 values?
Also the force constants rk2 and rk3? Which force consant should be used in
calculating the harmonic potential?
Appreciate your help.

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Received on Sun Aug 19 2007 - 06:07:09 PDT
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