[gmx-users] Problems with the SHAKE-algorithm -> is a problem of energy conservation

Björn Fischer bjuwelix at netcologne.de
Tue Mar 7 16:16:43 CET 2006

David van der Spoel wrote:
> At high temperature you need a shorter time step. Are you sure you 
> don't want to use T-coupling?
Thanks for the advice,

it didn't solve the problem, but it took me one step further to the 
solution. I should have been more specific about my system:

Its an argon/nonane (2:1) system at 600 K. The normal timestep is 1.0 
fs, I also used 0.5 fs and 0.1 fs for testing purposes.
Only the argon is coupled to the heatbath.

The Shake-problem is only a symptom, the real problem is that the energy 
is not conserved (checked via a NVE-run).
The total energy is conserved for a time (for example about 60000 
timesteps) , then jumps upward fourfold over about 1000 timesteps.
After that the SHAKE-problems starts. Making the timestep smaller 
doesn't solve the problem.

Do you have any suggestions, why the energy is not conserved (apart from 
a wrongly implemented force field) ?

Thanks in advance for your help!

-- Björn

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