[gmx-users] Can I use Ryckaert-Bellemans parameters to build a multiple dihedrals topology
bianwenbo at gmail.com
Mon Jul 21 16:21:38 CEST 2014
[Sorry for the wrong-coding in last mail, I post it again.]
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 in OPLSAA force field) 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)
(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 ] section)
(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)
Thank you for your time!
What’s more, I've read the following discussions but still have no idea.
- [gmx-users] constant term in dihedral potential function - May 29 2009
- [gmx-users] Type 9 dihedral in Gromacs topology - Oct 27 2012
- [gmx-users] Re: dihedraltypes funct 4 and 9 in gmx 4.5 amber - Aug 19 2010
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