[gmx-developers] virial

Jason de Joannis jdejoan at emory.edu
Thu Jan 11 18:13:27 CET 2007

Hi David,

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:
>>  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
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\ Jason de Joannis  \
\ Emory University  \
  \ jdejoan at emory.edu \
   \ 404-402-1332      \

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