VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Tue Jan 02 2018 - 09:31:43 CST

Dear Jadzia,
The reason that the order is reversible is that the way the improper
potential is defined is based on the angle between the plane containing the
first three atoms, and the plane containing the second three atoms (see
Fig. 2 of http://onlinelibrary.wiley.com/doi/10.1002/jcc.540040211/epdf).
Those planes are not changed by reversing the order of the atom list (since
the first three simply become the second three and vice versa).

I am not sure, though, whether the implementation of the improper angle
calculation used by all programs compatible with charmm-style psf files is
the same. Some aspects of the charmm documentation strongly suggests that
it requires the central atom to be listed first, and cp2k may be the same
way. This may reflect different implementations of how to calculate the
angles, or may be due to the valid concern that the reversibility does not
hold except under special cases of the improper potential (it is only true
for the harmonic potential with a phase angle of 0, but that condition is
satisfied for all cases in the charmm parameter sets). For the harmonic
version of the improper potential with that phase angle condition
satisfied, I don't see why they should not ultimately work out the same
under strict reversal of the atom list.

Best,
Peter

On Tue, Jan 2, 2018 at 2:29 AM, Jadzia Dax <jadziadax30_at_gmail.com> wrote:

> Hi Everyone, and a happy new.
>
> On this
> <http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node24.html>
> NAMD/VMD page here is written:
>
> *As with dihedrals, the order of atoms within an ​​improper may be
>> reversed. As shown below, impropers are specified by the IMPR statement
>> followed by sets of four atoms, with the central atom to which the other
>> three are bonded typically listed first.​*
>
>
> Why can the direction be reversed with impropers? As far as I can see this
> would change the central atom. The three orbital atoms should be
> exchangable of course, but this would rather be any permutation of the last
> three atoms.
>
> The reason why I am concerned with this topic is that I have rtf/prm files
> for a ligand prepared with CGenFF. The rtf file has one Improper. And when
> I create the psf file with VMD/psfgen then the psf file has the atoms in
> reversed order than in the rtf-file. But the prm-file still has the
> original order. Thus my simulations (not with NAMD but with CP2K) fail
> immediately because the it cannot find the parameters for this improper.
>
> Any help or comment is appreciated.
>
> Best wishes,
> Jadzia
>