Re: fixed bond length

From: Ajasja Ljubetič (
Date: Fri May 11 2012 - 11:06:35 CDT

Dear Mortaza,

The stiffer the spring the quicker it will oscillate, so perhaps you could
reduce your time step in order to keep the integration stable?


On 11 May 2012 17:51, Mortaza Aghtar <> wrote:

> 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
> questions:
> 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.
> Meisam

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