[gmx-users] explicit hydrogen-bond

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Jan 31 13:45:25 CET 2007

Hi Andrea,

You should also note that there is a fundamental difference between a
crystal structure and a system in solution. Hydrogen bonds which are
more or less exposed to the solvent will have a much more transient
character in solution than in a crystal. Adding a hydrogen bond
potential is an artificial measure to try to keep close to the crystal
structure. That may not properly reflect the ensemble you're after.



On 1/31/07, Lars Schaefer <Lars.Schaefer at mpi-bpc.mpg.de> wrote:
> Hi andrea,
> since your Hbond breaks rather early it could be that your system is not
> completely equilibrated, which could impose some strain on the bond. You
> could put a distance restraint on that Hbond (and others that are
> supposed to be imortant) and run for a while before your production
> simulation.
> Lars
> andrea spitaleri wrote:
> > Hi all,
> > I have a question concerning the H-bond. I am running a protein-peptide
> > simulation in water.
> > My starting structure is a X-ray complex. What I am observing is that
> > after 200ps an important hydrogen bond between the peptide and the
> > protein is breaking (ARG -- ASP). Now, since experimental data and
> > previous MD (using CHARMM as ff) have demonstrated that this hydrogen
> > bond is very important for the interaction, I am concluding that in my
> > case I have a problem with my used ffG43a1.
> > I have been reading few papers and I see that CHARMM ff uses an explicit
> > hydrogen-bond contribution in the calculation. From the gromacs manual
> > there is not note about it. In order to validate my assumption, I am
> > thinking either to swap to ffopls or to perform a small dynamics at low
> > temperature and increase it to 300K to allow a better equilibrium.
> >
> > Any suggestion are very welcome.
> >
> > Regards
> >
> > thanks
> >
> > andrea
> >
> >
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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