From: Joe Yelk (joseph.yelk_at_colorado.edu)
Date: Tue Oct 18 2011 - 17:46:57 CDT
Hello,
I wanted to make sure that I understand how to use structure and parameter
files in X-Plor format for multiple dihedral angles. To test this, I
created a pdb file of hexafluoroethane (C2F6) that was minimized using a QM
package. I set k=1, n=1, and delta=0.0 for the F C C F dihedral. The
dihedral energy as calculated by NAMD was 9.0000. This makes sense for a
potential of k*(1+cos(n*phi)) because there are 9 dihedral angles, and the
cosine terms should cancel because of the symmetry.
Next, I duplicated the listing of each dihedral in the psf file. I also
doubled the number of dihedrals listed in the psf file (from 9 to 18). I
modified the parameter file to include an extra dihedral, and set k for this
dihedral to zero. NAMD reported the dihedral energy to be 18.0000. I
expected the energy to still be 9.000, since the additional parameter was
set to zero.
Using a third dihedral parameter with k=0.0, we get 27.000. Setting all k's
equal to zero produces a dihedral energy of 0.0000.
I could just divide all the dihedral k's by the multiplicity, but I couldn't
find anything about this in the X-Plor or NAMD manuals. Is that what I need
to do, or is there something else wrong? Thanks for your help.
Sincerely,
Joseph Yelk
*Original PSF:*
9 !NPHI: dihedrals
3 1 2 6 3 1 2 7
3 1 2 8 4 1 2 6
4 1 2 7 4 1 2 8
5 1 2 6 5 1 2 7
5 1 2 8
*Original parameter file:*
DIHEDRAL F C C F MULTIPLE=1 1.0 1 0.0
*Modified PSF*
18 !NPHI: dihedrals
3 1 2 6 3 1 2 7
3 1 2 8 4 1 2 6
4 1 2 7 4 1 2 8
5 1 2 6 5 1 2 7
5 1 2 8 3 1 2 6
3 1 2 7 3 1 2 8
4 1 2 6 4 1 2 7
4 1 2 8 5 1 2 6
5 1 2 7 5 1 2 8
*Modified parameter file:*
DIHEDRAL F C C F MULTIPLE=2 1.0 1 0.0
0.0 3 0.0
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:57:50 CST