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

Alex nedomacho at gmail.com
Thu Jul 13 03:12:24 CEST 2017

> 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.


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