[gmx-users] Purpose of repeated improper dihedrals

[Dawid das]

OK, I see. Thanks again!

pt., 2 sie 2019 o 17:07 Justin Lemkul <jalemkul at vt.edu> napisał(a):

>
>
> On 8/2/19 8:59 AM, Dawid das wrote:
> > Thank you for an asnwer. However, I still need to ask more.
> > So, let's take this time the
> > NR1  CPH1  CPH2  H
> > NR1  CPH2  CPH1  H
> >
> > example. For such quartets,  the improper dihedral parameters are defined
> > for HSD residue.
> > Now, the bonding is as follows in part of HSD:
> >            H
> >            |
> >          NR1
> >        /        \
> >   CPH1    CPH2
> >
> > In my top file generated with pdb2gmx I can see the improper dihedral
> > entries for both
> > NR1  CPH1  CPH2  H
> > NR1  CPH2  CPH1  H
> > Also after dumping the tpr file I can see IDIHS entries for both
> > arrangement of atoms for the same molecule.
> >
> > According to Gromacs manual, the entry for improper dihedral i j k l is
> > understood as follows
> >          l
> >          |
> >          i
> >        /   \
> >      j      k
> >
> > So maybe I'm blind but I still don't really understand  the purpose of
> > changing the middle atom types
> > if there is in fact only one way these four atoms are connected in HSD.
> The
> > only reason I see is to
> > make it more rigid because I have "doubled" improper.
>
> Again, I would not call it a "doubled" parameter, because they are
> clearly different in atom order. This usually implies a difference in
> stereochemistry; in this case, I don't know the history of why the
> impropers are assigned this way, but going back to the original CHARMM
> topologies there are in fact two impropers assigned around ND1, CD2, and
> CE1. The use of two terms with the same parameters but different
> connectivities is probably due to having to avoid some kind of
> asymmetry, though it seems unusual. Regardless, it is a faithful (and
> correct) representation of the force field and we have tested it for
> agreement between CHARMM and GROMACS.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
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>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
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