Discrepency in cell volume? Cell origin can move in NPT?

From: Edward Patrick Obrien (edobrien_at_Glue.umd.edu)
Date: Sun Apr 25 2004 - 12:56:36 CDT

  I was hoping someone could explain to me this apparent discrepency:

I did an equilibration run and the final volume, stated in the .log file,
is 49698.7591 angstroms^3.

I read the .coor file into vmd and calculated the cell volume by selecting
all the atoms in the system using the 'min-max' tcl function to calculate
the cellvectors: the cell volume from this calculation is: 55,706
angstroms^3 !

   What is the deal? 49698.7591 angstroms^3 compared to 55,706 angstroms^3
is a BIG difference.

   I really need to understand this discrepency because I want to ensure
the water density is OK.

   Also the cellOrigin moved during the NPT simulation from

   cellOrigin -0.14305 0.47288 0.31587

   before the simulation, to

   vmd > measure center $system
   cellOrigin 0.211786702275 0.572636842728 0.261837869883

   after the simulation... the cell origin was suppose to remain unchanged
I thought.

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