[gmx-users] reading topology by Gromacs

[Mohsen Ramezanpour]

Dear Gromacs users,

I want to add the modified parameters for several proper dihedrals.

So, I want to add them to the section [ dihedraltypes ] in ffbonded.itp.

There are two dihedrals already for the combination I want:

C       HC       HC      NC2     2     0.000000     0.000000
.
.
.
NC2        X        X        C     2     0.000000   376.560000


If I have the following dihedral (just for the sake of example):

C       HC       HC      NC2     2     angle     force_constant

Where shall I add this line exactly?

Since the angles can be either 0 or 180 in Charmm36, the parameters for:

C       HC       HC      NC2
should be the same with:
NC2      HC       HC     C

In other words, does Gromacs take the first or the last match it finds in
ffbonded.itp for the assigned atom types in desire dihedral?


I had a look at .tpr file using gmx dump, and I just can see the the
type number, e.g. 574, but I do not know where can I see the parameters for
these types (for gromacs version of Charmm36FF).

Thanks in advance for your comments

Cheers,
Mohsen






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