AW: fixed bond length

From: Norman Geist (
Date: Mon May 14 2012 - 01:23:05 CDT

Maybe you could use extrabonds with a high force constant.


Norman Geist.


Von: [] Im Auftrag von Aron Broom
Gesendet: Freitag, 11. Mai 2012 20:25
An: Mortaza Aghtar
Cc: Ajasja Ljubetič;
Betreff: Re: namd-l: fixed bond length


To do this properly you need to have the equations of motion solved such that those bonds are fixed, not just have stiffer springs. For instance, this is how SHAKE fixes the bond lengths of hydrogens. I'm not sure how hard it would be to have a custom SHAKE that applied just to your particular bonds of interest.


On Fri, May 11, 2012 at 12:29 PM, Mortaza Aghtar <> wrote:

Dear Ajasja,
That is true :). Reducing the time step solved the problem. Thank you.



On Fri, May 11, 2012 at 6:06 PM, Ajasja Ljubetič <> wrote:

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.



Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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