Calculate MSDs during MD run

Johannes Wagner joh... at
Sat Aug 1 17:18:06 UTC 2015

To specify a bit. Lets say I have a normal trajectory that looks like this:
      Cryst x
 i =        0, time =        0.000, E =       -16.1066791009
  O         4.4494725764        0.8609855793        6.0981987308
  O         3.8029095709        2.7229831166        4.5699381898
  O         4.0118989226        2.7023681308        1.2194938263
  O         6.0462348498        3.2953089592        5.9203028333
  O         3.2241009956        5.5031225318        4.3400008035
with 1000 steps inside.
Now I want to calculate the MSD with reference to the first configuration, 
how do I do that?

If I do this

           STEPS 1000
          TIMESTEP 1
           FIRST_SNAPSHOT 1
           LAST_SNAPSHOT 1000
                 &END MSD_KIND
          &END PRINT
          &MSD T
           &END MSD_PER_KIND    
         &END MSD

I only get this error

 *** ERROR in initialize_msd_reftraj (MODULE reftraj_util) ***

 *** End of reference positions file reached ***

however there are definitly 1000 steps in the file I link..

Anything else I need to consider? My question still stand if I can do this 
during the an ordinary MD run.. so not calculating the trajectory first and 
then letting the reftraj code run over it but have it as a normal output at 
the end of the run.

Thanks again and best regards,
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