fixed bond length

From: Mortaza Aghtar (
Date: Fri May 11 2012 - 10:51:01 CDT

Dear all,
I want to run NAMD for a system with fixing length of some bonds. So I did
it with defining a high spring constant value for those bonds. What
happened was that when I define the constant values up to 15000
kcal/A**2/mol there is no problem for equilibrating system but bonds
fluctuate around 0.03 A (less than before). And when I increase the spring
constants there is an error about atoms moving too fast. The error is not
solved by either minimizing the system or setting Margin. I have two

1- Is there any other way to fix the bond lengths other than increasing
spring constant while it can make other problems? There might be a method
similar to the rigid bond option for hydrogen atoms.

2- If that is the only way, how can I solve the error?

Thanks for your consideration.


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