[gmx-developers] Use of pbc_dx in bonded calculations

David van der Spoel spoel at xray.bmc.uu.se
Tue Sep 21 08:57:19 CEST 2004

On Tue, 2004-09-21 at 07:34, Vishal Vaidyanathan wrote:
> Hi,
>    I'm working on gmx 3.1.4 and I see that the bonded functions use
> pbc_rvec_sub() to calculate the bond vectors. Is this necessary? It seems
> that shift_self() is called to make molecules whole before the bonded
> functions in do_force(), so a simple vector difference should give the
> same result as pbc_dx() right?
>    If this is not true, could somebody let me know what exactly
> shift_self() does?

This is true, but in some case we need to have "normal" periodic
boundary conditions computed, e.g. when we have infinite molecules.
Therefore we need some flexibility in calling the pbc routines. Some of
this stuff has changed in 3.2 by the way.

>    Any help is appreciated!
>    Thanks,
> Vishal
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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