[gmx-users] Purpose of repeated improper dihedrals

[Dawid das]

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.

Best regards,
Dawid Grabarek

pt., 2 sie 2019 o 13:40 Justin Lemkul <jalemkul at vt.edu> napisał(a):

>
>
> On 8/2/19 2:38 AM, Dawid das wrote:
> > Dear All,
> >
> > Why some of the improper parameters in CHARMM27 FF are repeated with
> > the middle atom types in a different order as in, e.g.
> >
> > HR1     NR1     NR2     CPH2    2       0.0000  4.184
> > HR1     NR2     NR1     CPH2    2       0.0000  4.184
>
> These aren't repeated parameters. They are different parameters
> corresponding to different connectivity.
>
> -Justin
>
> > while some are not, e.g.
> > HR3     CPH1    NR3     CPH1    2       0.0000  8.368
> >
> > Best regards,
> > Dawid Grabarek
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>