[gmx-users] integration scheme
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
>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
>> 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?
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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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