AMBER Archive (2007)

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

From: Sudha Mani Karra (karra.md_at_gmail.com)
Date: Wed Aug 15 2007 - 10:40:37 CDT

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

&cntrl
   imin=0, irest=1, ntx=7,.......,
   .........,
 &end
 &rst iat=1, 6, r1=0.0, r2=..., r3=..., r4=...,
      rk2=....,rk3=.....
 &end
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.
Sudha

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