[gmx-users] dihedraltypes funct 4 and 9 in gmx 4.5 amber ff

Mark Abraham mark.abraham at anu.edu.au
Tue Aug 17 14:18:44 CEST 2010

----- Original Message -----
From: Alan <alanwilter at gmail.com>
Date: Tuesday, August 17, 2010 21:24
Subject: [gmx-users] dihedraltypes funct 4 and 9 in gmx 4.5 amber ff
To: Gromacs <gmx-users at gromacs.org>

> Hi there,
> I've been looking at amber ff implementation of gmx 4.5 since I am familiar to Sorin's ffamber works and I am the developer of ACPYPE.> 
> I noticed that proper dih are not converted to RB anymore (which's great for understanding) and to accomplish that apparently 2 new funct were added to the gmx code, namely 4 and 9.  > 
> Needless to say that I couldn't find anything about funct 4 and 9 in the current gmx manual.

Type 9 was added to facilitate CHARMM's multiple proper dihedrals, in git commit a7c597c778351f by Erik, whose message was 

    Added support for dihedraltype 9, which allows multiple terms for proper dihedrals.
    By listing a dihedral with type 9, grompp will now scan the force field to see if there are
    multiple terms on _adjacent_ lines listed in the dihedraltypes section, and in that case add them all.

A code snippet in src/kernel/toppush.c reads

        if(ft == 9)
                /* Previously, we have always overwritten parameters if e.g. a torsion
                 with the same atomtypes occurs on multiple lines. However, CHARMM and
                 some other force fields specify multiple dihedrals over some bonds,
                 including cosines with multiplicity 6 and somethimes even higher.
                 Thus, they cannot be represented with Ryckaert-Bellemans terms.
                 To add support for these force fields, Dihedral type 9 is identical to
                 normal proper dihedrals, but repeated entries are allowed.
                bAllowRepeat = TRUE;
                ft = 1;
> I would appreciate more information about it. Among other things I would like to know, e.g., what funct 4 would have different from funct 1, since in the seminal work of Sorin, amber impr. dih are treated as prop. dih in gromacs.
>From src/gmxlib/{ifunc,bondfree}.c and src/kernel/{topdirs,toppush}.c it can be seen that dihedraltypes 4 and 1 call the same evaluation function. Perhaps Erik can confirm this.

src/gmxlib/ifunc.c did suggest to me that something is not quite right...

  def_bonded  ("PDIHS",    "Proper Dih.",     4, 3, 3,  eNR_PROPER, pdihs         ),
  def_bonded  ("RBDIHS",   "Ryckaert-Bell.",  4, 6, 6,  eNR_RB, rbdihs            ),
  def_bonded  ("FOURDIHS", "Fourier Dih.",    4, 4, 4,  eNR_FOURDIH, rbdihs       ),
  def_bonded  ("IDIHS",    "Improper Dih.",   4, 2, 2,  eNR_IMPROPER,idihs        ),
  def_bonded  ("PIDIHS",   "Improper Dih.",   4, 3, 3,  eNR_PROPER, pdihs         ),
If PIDIHS is an improper dihedral with the functional form of a proper dihedral, should it not use eNR_IMPROPER?


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