[gmx-users] Are the output of velocity, force and position at the same time

[David]

On Thu, 2003-03-20 at 19:07, qiao rui wrote:
> hi,
> 	Maybe this is a old question, but I am curious whether the
> velocity and position output by Gromacs are at the same time. when I
> looked at the md.c, it reads:
> 
> 	...
> 	do_force();
> 	...
> 	write_trj();
> 	...
> 	update();
> 	...
> 
> 	Since Gromacs is using a leap-frog algorithm, the velocity and
> position are not available at the same time, I tend to guess that unless
> there are some interpolation in write_trj(), the output of velocity, force
> and position would not be at the same time. So I would guess that:
> 	velocity (t-dt/2)
> 	position (t)
> 	force    (t+dt)
Almost correct, but it is force(t) and energy(t). Only velocity is out
of sync.

> 
> 	In addition, has the output force considers the impact of the
> constraints?
No.


-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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