From: Paul R Brenner (pbrenne1_at_nd.edu)
Date: Fri Jun 17 2005 - 09:08:54 CDT
Thanks for the response Jan.
As I understand it the difference between scaled1-4 with a scaling factor of 1.0
and scaled1-3 is that the scaled1-4 looks for the second set of VDW parameters.
If the second set does not exist the normal VDW contribution is calculated
between 1-4 just as if I had specified scaled1-3.
Paul R Brenner, P.E.
Graduate Research Assistant
Computer Science and Engineering
The University of Notre Dame
Quoting Jan Saam <saam_at_charite.de>:
> Dear Paul,
> A scaling factor of 1.0 means that the 1,4 interactions are fully
> included. I've once spoken to Alek Mackerell about this issue and he
> emphasized the importance of this scaling factor in order to obtain
> correct results.
> Neveretheless the CHARMM force field specifies modified VDW interactions
> for some atom types. You can find these in the parameter file. Here is
> an example from the NONBONDED section:
> !V(L-J) = Eps(i,j)*[(Rmin(i,j)/r(i,j))**12 - 2(Rmin(i,j)/r(i,j))**6]
> !epsilon [kcal/mole]: Eps(i,j) = sqrt(eps(i) * eps(j))
> !Rmin/2 [A]: Rmin(i,j) = (Rmin(i) + Rmin(j)) / 2
> !atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
> C 0.000000 -0.110000 2.000000 ! ALLOW PEP POL ARO
> CT1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000
> For atom type C only the parameters epsilon and Rmin/2 are specified
> thus no scaling is applied for 1-4 interaction (they are fully
> included). For atom CT1 though, the additional parameters eps,1-4 and
> Rmin/2,1-4 are given. These values are used for 1-4 interactions.
> The problem with 1-4 interactions is that their nonbonded contribution
> is already partially included in the corresponding dihedral parameter.
> Scaling down the 1-4 VDW interaction can help avoiding double accounting
> is a means of fine tuning the force field. You actually only have to
> worry about it if you are adding new parameters to the force field.
> Hoping this helps,
> Paul R Brenner wrote:
> > I have been reading the recent J Comput Chem paper by Dr. Mackerell
> > (DOI 10.1002/jcc.20082) and am now questioning the mechanism by which
> > 1,4 interactions are included/excluded for proteins in NAMD.
> > Dr. Mackerell states: "1,4 Nonbonded interactions, involving atoms
> > separated by three covalent bonds, do have nonbonded contributions as
> > well as their spatial relationship being influenced by the internal
> > terms, including the dihedral term. However, different biomolecular
> > force fields treat the 1,4 nonbond interactions differently... The
> > all-atom CHARMM biomolecular force fields do not scale the 1,4 terms
> > (scale factor = 1).
> > With a scale factor of 1, are 1,4 LJ contributions fully included or
> > excluded in NAMD?
> >> From the NAMD Tutorial:
> > When the scaled1-4 exclusion policy is used (as it should with the
> > CHARMM force field) nonbonded interactions of atoms separated by
> > three bonds (i.e., atoms 1 and 4 in the chain 1-2-3-4) are modifed.
> > Even if the scaling factor for electrostatics is 1.0 (as it should be
> > for modern CHARMM force fields), special modified van der Waals
> > parameters are used for 1-4 pairs of atoms for which they are
> > specified
> > So how does 1,4 scaling work when there is a special set of 1,4 LJ
> > parameters specified? Will the special parameters be recognized if
> > scaled1-4 is not specified.
> > Any insight on the standard/best method for specifying the 1,4
> > interactions in NAMD using the CHARMM force field, would be
> > appreciated.
> > Thanks,
> > Paul R Brenner, P.E. Graduate Research Assistant Computer Science and
> > Engineering The University of Notre Dame
> Jan Saam
> Institute of Biochemistry
> Charite Berlin
> Monbijoustr. 2
> 10117 Berlin
> +49 30 450-528-446
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