[gmx-users] PMF from pull code, unexpected results

Michael Brunsteiner mbx0009 at yahoo.com
Thu Feb 24 15:47:06 CET 2011

> Michael: your mdp options indicated using US and my stance is that,   > using 
>US, you are incorrect to say that "And you will get the SAME   > result if you 
>do this calculation in one or in three dimensions   > (pulldim NNY or pulldim 

this has nothing to do with the mdp file ... i was talking about a 
purely hypothetical case, if you use pull = constraints, rather than
umbrella sampling you don't NEED to run the calculation, since, as i said
you can figure out the result in your head ... with constraints the "average"
force will always be the exact LJ force at that distance, and if you integrate
that you will necessarily end up with the original LJ potential, no
matter whether you do that in one or in three dimensions!
if you only have two spherically symmetric particles, with an interaction
energy that depends only on the distance, and no solvent then the 
"free energy" and the "energy" are identical (apart from the
entropic contribution discussed in the Neumann paper) ...

that means: if you COULD do this calculation with constraints (in 
practice you probably can't because there'd be too few DOFs and the temperature
would be ill defined) you SHOULD get identical results, independent of pulldim
... unless the term in eqn 6.1 is somehow included explicitly, but i can't see
that anywhere in the code ... 
> Nevertheless, I'm a little perturbed by 
> your call out for help from somebody else "in the know", so I'll leave   > you 
>at this point. Good luck.

thanks, doesn't look as if there was much interest, I guess I'll have to go 
back to my statistical mechanics textbooks...



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