VMD-L Mailing List
From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Mon Mar 07 2016 - 12:30:26 CST
Indeed, these results look strange. Based on this information alone, it is impossible to know what the issue is. Double check the vdW terms (contained within the Additional Associated Parameter Files”), the optimized geometry that you’re inputing as “PDB File”, check that the hessian calculation terminated normally. You might also run the optimization with the “Write debugging log” turned on, and look through the output.
> On Mar 3, 2016, at 11:32 AM, Mohan maruthi sena <maruthi.sena_at_gmail.com> wrote:
> Dear vmd users,
> I am using the fftk toolkit to generate parameters for my molecule. I have optimized the molecule and performed hessian calculations. When I am trying to generate bond parameters, the equilibrium bond length and K (force constant) values obtained are as shown below:
> !atom type Kb b0
> C C4 0.739 -0.001
> C C2 0.153 0.000
> I could not understand why the values are too low. The initial parameter file contains 0 values are Kb abd b0. Could please suggest some of the possible reasons for the observed weird values for Kb and bo.
> Thank your very much for a reply in advance
> Mohan Maruthi