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.
Cheers,
Tsjerk
On 1/31/07, Lars Schaefer <[EMAIL PROTECTED]> 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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