[gmx-users] explicit hydrogen-bond

[Lars Schaefer]

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
> 
>