[gmx-users] Adding hydrogens to united atom trajectories

Jon Kapla jon.kapla at mmk.su.se
Wed Oct 26 15:57:54 CEST 2011


I'm performing united atom simulations of sugars and lipids and 
comparing calculated properties like C-H dipolar couplings and order 
parameters with corresponding results from experiments. To do this I 
need to calculate the hydrogen postitions of the hydrogens I'm 
interested in, and have previously used the gromacs protonate tool for 
this. Since some time this tool seems to be quite broken, so I've 
written my own routines for the calculations.

Now to my concern. The gromacs tool seems to have used a fixed H-C-H 
angle of 109.5 degrees when adding CH2-group hydrogens. I'm sure that 
this is an approximation as good as anything, but shouldn't a better 
approach be to let the H-C-H angle vary with the corresponding C-C-C or 
C-C-O angle?

I've done some searching regarding this, and I've found these two articles

 MASTRYUKOV, V.; OSINA, E. Journal of Molecular Structure. 1977, 36, 
 Dakkouri, M. Journal of Molecular Structure. 1997, 413-414, 133-152.

stating the following empirical relationship between the angles (the 
second article is citing the first) as an approximation of the angle 
correlations fitted from diffraction data:


A C-C-O angle of 113 degrees would with this relation give a H-C-H angle 
of 106.3 degrees.

Does anyone have any thoughts about this?

Jon Kapla


Jon Kapla
   Division of Physical Chemistry
   Dpt. of Materials and Environmental Chemistry (MMK)
   Arrhenius Laboratory
   Stockholm University
   SE-106 91 Stockholm
Pos:    PhD Student
Phone:  +46 8 16 11 79 (office)
Phone:  +46 70 304 19 89 (cell)
E-mail: jon.kapla at mmk.su.se

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