[gmx-users] Periodic Molecule's Free Energy Calculation Error

[Alex]

>
> I wonder if the "couple-intramol = yes" is a must. Does it have any 
> influence on the output results if we turn off the intra-molecular 
> non-bonded interactions of a large infinite molecule?
>
The answer to your question has nothing to do with Gromacs, but with 
understanding the difference between crystals and biomolecules (for 
which Gromacs was designed).
Also (unrelated), it is a common misconception to believe that PBC makes 
something infinite -- the effective size of your system is entirely 
determined by the supercell size (proof: consider the ripples in hBN and 
determine the lowest wavelength of the ripple that can propagate -- it 
is commensurate with the box size). In an infinite system, you can have 
an immensely long wave (though not infinite, as shown by Landau a while 
back). PBC does not make anything infinite, it is a mathematical way of 
avoiding surfaces.
>
> There is no universal force field for HBN, so I am using a modified 
> gromos54a7_atb force field, i.e., manually adding the parameters for 
> boron and nitrogen to the bonded & nonbonded .itp files.
Oh, I know that there is no force fields for these structures. ;) My 
question was about which Gromacs ff you were using to insert your 
parameters, and, most importantly, where those parameters came from.

> The parameters are obtained from literature.
>
What literature? All bio-style ff adaptations of solid-state potentials 
(e.g. Tersoff-Brenner for hBN) I am aware of make it very clear that 
"intramolecular" interactions between atoms sharing up to a fairly 
distant covalently bound neighbor are limited to bonds and angles. This 
comes from the math involved in developing potentials for crystals. 
There was a recent question regarding this very problem here, which was 
solved by setting a larger nrexcl value. In your case, you solved it 
with turning off intramolecular coupling. In fact, if you set your 
nrexcl to something like 4 or 5, you may not even need to turn off the 
coupling. But then again, I don't know where the parameters came from.

Alex