Archive from user: Xiang Zhong I believe it is a known issue, in free energy calculation for the dihedral type **5**, it will pop up some error information complaining that Fourier type dihedral is not implemented, like; \_Fatal Error: Function type Fourier Dih. Not implemented in ip\_pert\_ This error is mainly related with two files, \_src/gromacs/topology/topsort.cpp (line 139) src/topology/ifunc.cpp (line 111)\_ In the latter file, it has defined all the type of functions and parameters that Gromacs would use, in a way enumerating those constant-string-variables. For this definition, in topology file, under `[dihedrals]` directive using the calculation function type **5**, after executed **grompp** command, it by default will use Fourier type function to make binary **tpr** file. ```c"> gmx grompp –f *mdp –c *gro –p *top –o *tpr ``` if we use gromacs built-in command **dump** this file, we will find some lines in key word “fourdihs” showing the dihedral type will be used. <code class="c"> gmx dump –s *tpr > *txt [any free plain text file] ``` however, if we use dihedral function **3**, which means **ryckaert-bellemans** dihedral type will be used for the calculation, the difference of it with the **fourier dihedral** is only the conversion difference. in gromacs manual **table 5.5**, using the cross-link we can easily find this transformation. if we define four coefficients of **fourier dihedral**; <code class="c"> v = 1/2*[ f1*(1+cos(phi)) + f2*(1-cos(2*phi)) + f3*(1+cos(3*phi)) + f4*(1-cos(4*phi)) ] ``` because of the trigonometric function, `cos(2*phi) = 2*cos^2(phi) – 1`, then the six **ryckaert-bellemans** will be calculated; <code class="c C0 = F2 + 1/2*(F1 + F3) C1 = 1/2*(-F1 + 3*F3) C2 = -F2 + 4*F4 C3 = -2*F3 C4 = -4*F4 C5 = 0 ``` If we follow the top procedure using a new topology file to make **tpr** file and **dump** it, using the key-word “RBDIHS”, we will know the dihedral calculation has been changed to **Ryckaert-Bellemans** for dihedral type **3**. However, this **tpr** file can be used for the Free Energy calculation without any problems. **Therefore, it comes a question, for Free Energy calculation, does it have calculation difference between Fourier Dihedral and Ryckaert-Bellemans for the same data but only at different mathematic conversion equations?** As far as I know, I don’t think they have any difference at the perturbation theory, since for bonded information calculation it is merely a factor of difference scale values. Besides, in code area, it seems the return parameter `bPert`, for the function `static gmx_bool ip_pert(int ftype, const t_iparams *ip)` in module `topsort.cpp`, is only a **bool** value. If not luckily, here comes two possible solutions: 1) Update the **grampp** command output result. In the **mdp** file, if `free energy` is turned on, during **grompp** command process, transferring dihedral type **5** to corresponded dihedral **3** in the topology file if it has any, then using these converted values to generate binary **tpr** file. In this way, which means no matter whether **Fourier Dihedral** or **Ryckaert-Bellemans** is set in the topology file, the final calculation will always be based on the **Ryckaert-Bellemans**. 2) Add **bool** return value for function `static gmx_bool ip_pert` (line 48) in `topsort.cpp` source file, as well as some other codes for the Fourier Dihedral perturbations. **NOTE** For the attached files, the same **gro** file and **mdp** file are used for **mdrun**, the difference is the **top** file, for these two **top** files, the differences are at \[dihedrals\] directives, in where different function types are selected. *(from redmine: issue id 2606, created on 2018-08-09 by gmxdefault)* * Uploads: * [dump_butane_tip4_dihedralType_3.tpr.txt](/uploads/6077bf7988bf5559957b6c6fa737ee99/dump_butane_tip4_dihedralType_3.tpr.txt) dump -- binary tpr file for dihedral type 3 -- Ryckaert-Bellemans * [dump_butane_tip4_dihedralType_5.tpr.txt](/uploads/e32bd0e89dcd8308f719988e916be282/dump_butane_tip4_dihedralType_5.tpr.txt) dump -- binary tpr file for dihedral type 5 -- Fourier Dihedral * [butane_tip4_dihedralType_5.log](/uploads/132b62e6c77fe0ae2de7df4adde39946/butane_tip4_dihedralType_5.log) mdrun -- log file for dihedral type 5 -- Fourier Dihedral * [butane_tip4_dihedralType_3.log](/uploads/12c860eb5e03d18f5bd5d3f431eb967a/butane_tip4_dihedralType_3.log) mdrun -- log file for dihedral type 3 -- Ryckaert-Bellemans * [butane_tip4_dihedralType_5.tpr](/uploads/997dd02aaae7885ffcd4a2a3cc62cc69/butane_tip4_dihedralType_5.tpr) tpr file for dihedral type 5 -- Fourier Dihedral * [butane_tip4_dihedralType_3.tpr](/uploads/21db11a20e0b4d8a4fa4c455a7350c54/butane_tip4_dihedralType_3.tpr) tpr file for dihedral type 3 -- Ryckaert-Bellemans * [butane_tip4_dihedralType_5.top](/uploads/6d7676fc62b82696512082667512474f/butane_tip4_dihedralType_5.top) top file for dihedral type 5 -- Fourier Dihedral * [butane_tip4_dihedralType_3.top](/uploads/456a4fb9007b7361274d244627df4353/butane_tip4_dihedralType_3.top) top file for dihedral type 3 -- Ryckaert-Bellemans * [butane_tip4.gro](/uploads/d74a69e44a1aeb62d3fe148c8ce5a42f/butane_tip4.gro) gro file used for grompp comamnd to make binary tpr file * [grompp_npt_fep.mdp](/uploads/c6271d718cf63227daeec6c76b6b818d/grompp_npt_fep.mdp) mdp file used for grompp comamnd to make binary tpr file