> 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
>YYY)".
this has nothing to do with the mdp file ... i w
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 YYY)". Nevertheless, I'm a little perturbed by
your call out for hel
Looking at http://www.brunsteiner.net/tbut-pmf.gif you seem to be
getting exactly what I would expect. The difference is the entropy
term. Note that the spherical shell increases volume as r increases
for pulldim YYY but this effect is absent for pulldim NNY. This is why
you can correct as
Dear all,
I would like to calculate the potential of mean force between two molecules
in aqueous solution using the pull code. For a start i performed a number
of calulations with a couple of very simple model systems with settings
loosely based on the example in the gmx tutorial section (see m
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