[gmx-users] questions about Ryckaert-Bellemans type dihedrals

[Mark Abraham]

Hi,

The only thing that matters is that you understand how the force field
constructs the interactions, and that your topologies do that :-)

Mark


On Tue., 9 Jul. 2019, 22:09 Yunhui Ge, <tuf74040 at temple.edu> wrote:

> Hi,
>
> I have a question regarding Ryckaert-Bellemans dihedral potentials
> (function type 3). In the manual of GROMACS 4.5.4 it says to use
> Ryckaert-Bellemans type, one needs to erase the 1-4 interaction in [pairs]
> section. My first question is what will happen if I use this potential
> (type 3) but leave the 1-4 interaction in [pairs] section?
> Next in the newer version GROMACS (5.1.4) the manual says:
>
> *In the original implementation of the potential for alkanes no 1-4
> interactions were used, which means that in order to implement that
> particular force field you need to remove the 1-4 interactions from the [
> pairs ] section of your topology. In most modern force fields, like OPLS/AA
> or Amber the rules are different, and the Ryckaert-Bellemans potential is
> used as a cosine series in combination with 1-4 interactions.*
>
> What force field is considered as most modern force fields? (I'm using
> AMBER ff99SB-ildn-nmr.) Again what will happen if I don't remove those 1-4
> interactions in the [pairs] section?
> My last question is should I expect huge differences between
> Ryckaert-Bllemans potential (type 3) and periodic (type 9) in simulations
> of the same molecule? I plan to run some simulation to test that but I
> wonder if there is a general answer based on the previous experience. Based
> on the manual I know RB potential excludes 1-4 interactions whereas
> periodic type include 1-4 interactions. I'm not clear about the performance
> difference between these two dihedral types. Also if RB potential requires
> the exclusion of 1-4 interactions why the manual says in modern force
> fields it is used in combination with 1-4 interactions.
> I'm familiar about this part and I do hope to learn more about this. Thank
> you for your time in advance!
>
> Best,
>
> Yunhui
>
>    1.
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