From: Axel Kohlmeyer (
Date: Mon Dec 02 2013 - 23:31:28 CST

On Tue, Dec 3, 2013 at 4:37 AM, sunyeping <> wrote:
> Dear all,
> In VMD the default cutoff value of a hydrogen bond is that the
> donor-receptor distance is less than 3.0 angstroms, and the
> angle formed by the donor atom, the hydrogen atom, and the receptor atom is
> less than 20 degrees. Will it be acceptable if I change the distance cutoff
> into 4.0 angstroms? Thanks.

acceptable for whom? or for what? and to show what? and with what justification?

this all has little to do with VMD but the science of hydrogen bonds,
so my suggestion is to read about this and look up how other
scientists have answered the questions from above and then make an
educated decision. remember, *you* have to defend the results and
"some guy on the mailing list said it is ok" doesn't look very good at
that time.


> Yeping Sun
> Institute of Microbiology, Chinese Academy of Sciences

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.