CHARMM params

[ilya]

On Nov 5, 11:40 pm, "willi... at gmail.com" <willi... at gmail.com>
wrote:
> Hi  Ilya,
>
> I think you should look elsewhere in your simulation input files. The
> negative force constant for UB is okay unless the implementation of
> charmm force fields is wrong in both namd and cp2k. Here are the intra
> potentials for ATP in the gas phase using a non equilibrated
> structure...
>
> Best of luck,
>
> will
>
> #CP2K
>  E_BOND =  1320.3740370591104
>  E_UB =  -17.003933895757882
>  E_BEND =  143.5847380741416
>  E_TOR =  32.03694034244833
>  E_IMP =  0.0011798180303465094
>
> #NAMD
> ETITLE:      TS           BOND          ANGLE          DIHED
> IMPRP
> ENERGY:       0      1320.3939       126.5827        32.0374
> 0.0012

Yes. Today I looked at NAMD code. It seems that there is no special
treatment of negative UB const. The equations in cp2k and namd seem to
be the same.
Moreover I found an article where they obtained these params:

A Molecular Mechanics Force Field for
NAD+, NADH, and the Pyrophosphate
Groups of Nucleotides.
Journal of Computational Chemistry, Vol. 18, No. 2, 221]239 (1997)

It states that consts were made negative intentionally.

I will keep searching.

Best wishes.
Ilya.