[gmx-users] integration scheme

Erik Lindahl lindahl at stanford.edu
Mon May 12 01:40:01 CEST 2003


Well, actually you can - the integration just becomes an equation that  
is straightforward to solve :-)

Our first version of Nose-Hoover was implemented that way, but we since  
changed it to use the temperature calculated from velocities last step.  
The reason for this is that it would otherwise be necessary to do extra  
communication when running in parallel, and the error is extremely  

I might add a switch so you turn this optimization off, but it will  
only make a difference if you are integrating something like a single  
harmonic oscillator...



On Friday, May 9, 2003, at 12:22 America/Los_Angeles, Lianqing Zheng  

> Dear Gromacs pals:
> This may be trivial, but I am curious. When Nose-Hoover temperature
> coupling is used, the accelerations are dependent on velocities, then
> regular leap-frog algorithm can't solve this kind of equations. This is
> because:
> v(t+0.5*dt) = v(t-0.5*dt) + a(t)*dt
> however a(t) depends on v(t), which is unknown at this time.
> How does Gromacs do with it?
> Thanks!
> Lianqing
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Erik Lindahl, MSc, PhD     <lindahl at stanford.edu>
D109, Fairchild Building
Dept. Structural Biology, Stanford University School of Medicine
Tel. 650-7250754    Fax. 650-7238464

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