[gmx-users] gromacs 3.3 user-defined potential functions

[Nikolai Smolin]

Hello Gromacs user,
I want to use user-defined potential functions for repulsion, dispersion 
and Coulomb.

in manual i found that I have to prepare table:
This file
should contain 7 columns: the x value, f(x), -f(2)(x), g(x),
-g(2)(x), h(x), -h(2)(x), where f(2)(x) denotes the 2nd
derivative of function f(x) with respect to x. f(x) is the Coulomb
function, g(x) the dispersion function and h(x) the repulsion function.

for example for L-J (12-6)
h(x) = (1/x)**12 (positive)
-h(2)(x) = -(-12)*(-13)*(1/x)**14 (negative)

but in file /gromacs/share/gromacs/top/table6-12.xvg


0.04                25    31250    -2.44141E8    -6.40869E12    
5.96046E16    5.81145E21
0.042    23.8095    26994.9    -1.82181E8    -4.33765E12    
3.31901E16    2.93518E21
0.044    22.7273    23478.6    -1.37811E8    -2.9897E12    1.89919E16    
1.53034E21
0.046    21.7391    20547.4    -1.05549E8    -2.09501E12    
1.11405E16    8.21325E20
0.048    20.8333    18084.5    -8.17622E7    -1.49046E12    
6.68506E15    4.52634E20
0.05               20        16000           -6.4E7     -1.0752E12     
4.096E15        2.5559E20
0.052    19.2308    14223.9    -5.05801E7    -7.85638E11    
2.55835E15    1.47597E20
0.054    18.5185    12701.3    -4.03309E7    -5.80897E11    
1.62658E15    8.70186E19
0.056    17.8571    11388.5    -3.24244E7    -4.34255E11    
1.05134E15    5.22989E19

you can see that values of h(x) and -h(2)(x) positive
some where error ?
in manual or in table6-12.xvg?

any suggestions

With best regard
Nikolai Smolin


-- 
----------------------------------------------------------------------------
Dipl.-Phys. Nikolai Smolin

Computer simulation of biomolecular system.

University of Dortmund
Department of Chemistry
Physical Chemistry I  -  Biophysical Chemistry
Otto-Hahn Str. 6
D-44227 Dortmund
Germany

Office:   C1-06 room 401

Phone:  +49 231 755 3929
Fax:    +49 231 755 3901

Phone:  +49 231 379 9635
mobile: +49 176 240 089 86

E-mails:            smolin at pci.chemie.uni-dortmund.de
            nikolai.smolin at uni-dortmund.de
            nikolai.smolin at udo.edu
            nikolai.smolin at gmail.com 

WWW:     http://pci.chemie.uni-dortmund.de/~smolin/
----------------------------------------------------------------------------