[gmx-users] H-bond in UA

David L. Bostick dbostick at physics.unc.edu
Tue Mar 23 15:20:01 CET 2004

Hello Henrik,

In some cases the UA force field can give an adequate enough representation
of the molecules to discern hydrogen bonding. Some recent works done by me
and my co-workers describe how to analyze hydrogen bonding in systems with
UA lipids both with energetic criteria:

(1) Biophysical Journal 86:1345-1356 (2004)

and with geometric criteria:

(2) Biophysical Journal 85:3120-3131 (2003)

We show in #1 that the energetic criteria can give the appropriate
distance and directionality for the united atom hydrogen bonds (even for
the CH..O hydrogen bond). Thus, it is probably okay to stick with geometric
criteria for discerning hydrogen bonds for the UA force fields. One cannot
say if it is okay in ALL cases, but in these works, it is demonstrated to
be reasonable.


David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick

On Tue, 23 Mar 2004, Henrik Rundgren wrote:

> Hello,
> I have a question concerning the H-bond.
> I haven't been able to find satisfying answers to the H-bond affect
> wilst using united-atom FF's. Some of them should explicit the polar H,
> but how well do they work?
> To simulate a cyclic peptide which includes the nonconventional a.a's
> ABU, SAR, MEXXX I apparently "have" to use the UA FF. Or does anyone
> have these a.a's in their all-atom FF's?
> NMR studies shows that there is several H-bondsin my peptide, how well
> would the united-atom FF take thses into account? It is essential for
> the structure that they are present.
> sincerely,
> henrik
> --
> _________________________________________________________________
> Henrik Rundgren
> Division of Physical Chemistry
> Arrhenius Laboratory
> Stockholm University
> S-106 91 Stockholm
> Sweden
> E-mail:    Henrik at physc.su.se
> Telephone: +46-(0)8-16 12 63
> Fax:       +46-(0)8-15 21 87
> Website:   www.fos.su.se/~henrik
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