Hello,
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).
I did some tests using Gromacs and it seems that I can specify the directive
[ 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
works?
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?
Thank you very much for your kind consideration,
Ana West
Emory University, U.S.A
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