[gmx-developers] virial

[David van der Spoel]

Jason de Joannis wrote:
> Let me revive an old topic concerning the fshift correction
> to the virial. This term is added up in the calc_vir function and
> I believe it is equivalent to the second term in Eq(2) of the 2005 
> Gromacs paper or Eq. B.11 of the manual. Since that term is
> rather simple it should be easy to check with the following snippet of 
> code:
> 
>  clear_mat(virtest);
>  for (n=start; n<start+homenr; n++)
>    for (i=0;i<DIM;i++) for (j=0;j<DIM;j++)
>      virtest[i][j] -= 0.25*box[i][i]*graph->ishift[n][i]*f[n][j];
> 
> Unfortunately I am not getting the same number for the trace of the
> virial tensor. Any suggestions would be appreciated.
> 
> /Jason

Do you have a rectangular box? Otherwise you need to use box[i][j].

Have you run mdrun with -debug? It will print temp variables to mdrun.log.

-- 
David.
________________________________________________________________________
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://folding.bmc.uu.se
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