[gmx-users] extracting bond streching parameters

Markus O Kaukonen mokaukon at cc.helsinki.fi
Thu Jun 20 10:35:32 CEST 2002

Dear all,

I did 'pdb2gmx' using
> 1 Gromacs Forcefield with all hydrogens (proteins only)

after 'grompp' one gets binary topology file 'topol.tpr'
which one can look at by 'gmxdump -s topol.tpr'

So finally to the question:

How do the following lines in the output of 'gmxdump'
>functype[81]=BONDS,b0A= 1.00e-01,cbA= 3.74e+05,b0B=1.00e-01,cbB= 3.74e+05
transform to bond streching parameters
k^b_ij and b_ij for each atom type pair ij
(ie. to parameters in eq. 4.33-4.34 in pdf manual ver. 3.11)?

Have a nice midsommer!, Markus

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