[gmx-developers] Molecular vs atomic virial

David spoel at xray.bmc.uu.se
Sat Oct 15 19:38:04 CEST 2005

On Sat, 2005-10-15 at 17:05 +0200, ramon at juguete.quim.ucm.es wrote:
> As I came late to this discussion, I do not fully understand it.
> >From the point of view of a molecular dynamics program, it is
> logical to consider atomic virial. Conceptually there is no such
> thing as a molecule for MD, only atoms bound by forces and constraints.
> What is the problem with working with atomic virial and pressure?
Whether or not to use an molecular or atomic virial. The molecular
virial is very unpractical and close to impossible to implement in
combination with different pressure scaling algorithms and constraints.
However it could be an option to scale molecular coordinates only when
doing pressure scaling, so as not to induce constraint errors due to
pressure scaling.

Maybe you can trace the discussion back in the archives if you want to
know more.
> Ramon
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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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