[gmx-users] Can I use Ryckaert-Bellemans parameters to build a multiple dihedrals topology
mark.j.abraham at gmail.com
Wed Jul 23 22:27:34 CEST 2014
On Mon, Jul 21, 2014 at 1:20 PM, rss <rss at leobian.com> wrote:
> Dear all,
> I want to get a “multiple dihedrals” topology file, but encounter a
> problem. The following are the details.
> I got the dihedrals parameters of azobenzene (expressed
> in Ryckaert-Bellemans form) from ‘DOI:10.1007/s00214-012-1274-z’
> (including cis-, trans-, and mixed).
> And in section ‘4.1.12 Proper dihedrals’ of Manual (v4.6.5), I found that
> function type 9 could be used for this purpose. It says "Type 9 allows
> multiple potential functions to be applied automatically to a single
> dihedral in the [ dihedral ] section when multiple parameters are defined
> for the same atomtypes in the[ dihedraltypes ]section.”, note that the
> function is expressed in the form of V_d(phi_ijkl) = k_phi (1 + cos(n*phi
> - phi_s)), which is different from the R-B form.
> Here are my questions:
> (1). Without ‘Type 9’, can I use the R-B parameters to get a multiple
> dihedrals topology file? (i.e. write both two lines of the cis- and trans-
> parameters under [ dihedrals ] section)
Maybe. I would not be surprised to learn the implementation of type 9 only
anticipated non-R-B dihedral functions. Either way, I'd make a system with
a single azobenzene, compute a single-point energy, and test what happens
as you change what you've specified in the topology. Testing is much more
reliable than documentation ;-)
(2). If not, can I use the mixed R-B parameters without ’Type 9' to achieve
> the same purpose? (i.e. only write the mixed parameters under [ dihedrals ]
> (3). If still not, how can I transform the R-B form into the Type 9
> function form? (i.e. from C0 - C5 to k_phi, phi_s)
Generally, you will not be able to do that. If you can do it, then
high-school trigonometry is your friend.
> Thank you for your time!
> What’s more, the following discussions maybe helpful for this question.
> - [gmx-users] constant term in dihedral potential function
> <https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-May/042279.html> - May
> 29 2009
> - [gmx-users] Type 9 dihedral in Gromacs topology
> <https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-October/075867.html> - Oct
> 27 2012
> - [gmx-users] Re: dihedraltypes funct 4 and 9 in gmx 4.5 amber
> <https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2010-August/053298.html> - Aug
> 19 2010
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