[gmx-developers] Pull code and virial

Justin MacCallum jlmaccal at ucalgary.ca
Sun Feb 27 21:17:47 CET 2005


I think I've discovered a problem with the way the pull code interacts 
with pressure coupling. As far as I can tell the extra forces added by 
umbrella sampling and AFM pulling are not included in the virial, 
leading to unexpected volume changes in the system when the 
thermodynamic mean force is high.

I'm not totally sure how to fix this. Is moving the pull code force 
calculation to before calc_virial enough? I'm not totally clear on how 
the virial is calculated in GROMACS.

I should point out that even when the man force is very high, the 
volume change is still quite small, on the order of one percent. This 
does however make a large difference in potential energy due to large 
changes in water-water interactions.

I don't think this a big problem for most simulations using the pull 
code, but if you want to look at volume changes, or potential energies 
there may be artifacts.


Justin MacCallum
PhD Student
Departement of Biological Sciences
University of Calgary

email: jlmaccal at ucalgary.ca
web: moose.bio.ucalgary.ca

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