Jason de Joannis
jdejoan at emory.edu
Thu Jan 11 18:13:27 CET 2007
Yes, I have a rectangular box. The debug file does print out all the fshift
contributions. But the bottom line is that when these are all totaled
and compared to the N-particle xshift[i]*f[i] calculation, things
should match up.
On a related note, but not one likely to resolve this situation, what
is the meaning of "we must in the implementation double the term
containing the shift delta-i" on page 182 of the manual? The equivalent
statement is not present on page 1709 of the Gromacs05 paper and I
don't see the sense of it.
Quoting David van der Spoel <spoel at xray.bmc.uu.se>:
> 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:
>> 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.
> 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 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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\ Jason de Joannis \
\ Emory University \
\ jdejoan at emory.edu \
\ 404-402-1332 \
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