[gmx-developers] RE: gmx-developers digest, Vol 1 #208 - 1 msg

Erik Lindahl lindahl at stanford.edu
Fri Aug 15 10:24:57 CEST 2003

On Friday, August 15, 2003, at 12:42 AM, Lakshmi Padmavathi wrote:

> Dear gromax developers,
> I would like to ask a question regarding the constraints again.
> If I no the distance between two atoms which are NON BONDED. Can I make
> a constraint for this during simulation? If it is possible could you
> suggest me that where can I define the constraints? Can I use shake
> algorithm for this. Please suggest me.

Constraining the distance would mean keeping it *exactly* at the value 
you specify, regardless of how much it would strain the rest of the 
molecule. This works great for bonds, but would probably not be a very 
good idea for nonbonded terms.

A better solution is to use distance restraints; this way you apply a 
potential if the distance deviates from the experimental value, and you 
can define how much it should be allowed to deviate and how hard the 
potential should be. Check the manual for details on how to use it.



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