[gmx-users] need help with free energy of solvation calculati on

David Mobley dmobley at gmail.com
Wed Jan 11 17:27:24 CET 2006


> Also, I saw somewhere in the manual that you need to define B state
> parameters for angles, torsions, etc. that involve perturbed atoms even if
> that particular interaction doesn't change.

I vaguely remember that this may have been something that was changed
in 3.3(perhaps now the default is to assume that the B state dihedrals
are the
same, when before it was to assume they were zero) but I can't find where I
read this so possibly I'm making it up. And I always repeat the parameters
in my own calculations just to make sure. (In 3.2, failing to repeat them
meant they were zero, which was bad).

Now I think my A and B states are being defined properly.  I am getting
> several warnings of this type from grommp:
> "No default Proper Dih. types for perturbed atoms, using normal values"

Yeah. I used to get that warning all the time, too. I think I had concluded
that it was OK. I don't seem to get it anymore so possibly there was a
"bugfix" that made the warning go away, but I can't recall for sure and I
don't have time to check right now.

Best wishes,
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