Ana West wrote:
I am trying to simulate a system composed of two different molecules. I
made the topology files for each of the two molecules and I did some
tests to validate the force-field parameters for my system. I do have
all the correct parameters for my system but it turns out that for the
two types of molecules I must use two different combination rules of the
LJ potential (the combination rule 1 and the combination rule 3).
That suggests you're mixing force fields, which is a bad idea. In any
case, you can convert between these parameter forms easily (see manual
section 5.3.3). Obviously, compare outputs between the old combination
rule parameters and the converted ones to check your conversion.
I did some tests using Gromacs and it seems that I can specify the
[ defaults ] only one time. The manual seems to indicate that I might
be able to do something about the combination rules by including a [
nonbond_params ] section in an *.itp file. However, I don;t seem to
understand the effect of the [ nonbond_params ] directive onto the [
defaults ] directive normally found in the *.itp file. It seems to me
that there is no combination rule specified in the under the [
nonbond_params ] section. Could someone please explain to me how this
There is one combination rule available, specified in [ defaults ] and
used everywhere required. This is sound methodology.
In addition/alternatively, does anyone have any suggestions on how I
could go about creating a successful set of topology files using two
different combination rules for the LJ potential?
Depending on the underlying reason, probably don't do it. For a start,
when an atom whose parameters are of combination type 1 interacts with
an atom whose parameters are of combination type 3, you would need to
pre-compute their interaction and describe that in [ nonbond_params ].
That's rapidly tedious as the number of atoms grows.
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