No difference between proper dihedral function type 1 and 9?

User discussions
1

GROMACS version: 2020.4
GROMACS modification: No

Hello all,

According to the GROMACS manual as specified here and here, the difference between function types 1 and 9 for proper dihedrals is that function type 9 allows for the defining of multiple potential functions (of different multiplicities) to a single dihedral type while function type 1 does not. However, I have found from my own tests that this does not appear to be the case in practice and am thus confused about the actual difference between these two function types. Let me elaborate.

In the Google Drive link below you will find two folders labeled “func1” and “func9” which contain identical files with the only difference being that the topology file in “func1” uses dihedraltypes function 1 while the topology file in “func9” uses dihedraltypes function 9. Please note that the topology file has multiple lines in the [dihedraltypes] directive that serves to assign multiple potential functions (of different multiplicities) to the same dihedral type. Using grompp, I have generated tpr files in each of the two folders and compared them using the dump command. From what I have seen, both tpr files appear to be identical (including the “Proper Dih.” section) and the tpr file utilizing dihedraltype function 1 actually has multiple entries listed in the “Proper Dih.” section for the same dihedral despite the fact that such functionality should be associated with function 9. Thus, there appears to be inconsistencies between what the manual states and what actually results in the tpr file according to the tests above.

https://drive.google.com/drive/folders/1uQEhWP2lin9b50t48piv0_1AQXQ0vkLk?usp=sharing

In such a case, is there actually any difference between proper dihedral function types 1 & 9 or is the manual not updated with regards to these sections? I ask this because lines 408 & 409 of the itp file $GMXLIB/share/gromacs/top/gromos54a7.ff/tmcl.itp attempt to assign multiple potential functions of different multiplicities to the same dihedraltype although function 1 is used on both lines. If there is actually a difference in implementation between functions 1 and 9, then wouldn’t this imply that the tmcl.itp file is incorrect? In addition, wouldn’t this make the GROMOS2016H66 forcefield (downloaded separately from here) implementation in GROMACS incorrect given that the latter uses dihedraltypes function 1 as specified in the [bondedtypes] directive of the 2016h66_orga.rtp file according to the screenshot below?

image
image546×835 90.2 KB

Sorry for the long post, but I hope I provided you with enough information to look into this and possibly answer my question.

Best,
Matthew

2

You have misunderstood how this works. You have assigned parameters on the line specifying the dihedral. Then there is no difference. Type 9 is to automatically assign multiple potential functions using a single dihedral line in the [ dihedrals ] section. The multiple potentials are looked up from the [ dihedraltypes ] section.