[gmx-users] integration scheme

Lianqing Zheng lzheng at me.rochester.edu
Mon May 12 02:37:00 CEST 2003

Thanks, Erik! Do you mean that you use a(r(t),v(t-0.5*dt)) instead of
a(r(t),v(t)) in the current version of Gromacs? I still don't get it how
it was in the first version. Could you please use equations to express it?

Sorry for the slow understanding... :D Thanks!


On Sun, 11 May 2003, Erik Lindahl wrote:

>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
>> _______________________________________________
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>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
>gmx-users mailing list
>gmx-users at gromacs.org
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list