From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Fri May 11 2012 - 11:06:35 CDT
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 <m.aghtar_at_jacobs-university.de> 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
> 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.
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:31 CST