[gmx-users] explicit hydrogen-bond

Lars Schaefer Lars.Schaefer at mpi-bpc.mpg.de
Wed Jan 31 13:09:27 CET 2007

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 


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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