[gmx-users] periodicity in gmx_msd.c

Pim Schravendijk schraven at mpip-mainz.mpg.de
Thu Oct 28 16:07:50 CEST 2004

Hello all,

I was recently looking into gmx_msd.c for the correction for periodicity 
and found two functions. I wonder why there is a 

  while(xcur[ind][m]-xprev[ind][m] <= hbox[m])
for prep_data_norm

 while (xcur[k][m]-xprev[k][m] <= -hbox[m])
for prep_data_mol.

For both there is the line:
   while(xcur[ind][m]-xprev[ind][m] >  hbox[m])

I guess that, since they should do the same, one of them is wrong, and the
prep_data_norm function seems to correct for periodicity in all cases,
even when the system looked at stays within one image-box, so imho there
should be a "-" added there.

Greetings, Pim

Pim Schravendijk - PhD Student
Max Planck Institute for Polymer Research

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