[gmx-users] explicit hydrogen-bond

andrea spitaleri spitaleri.andrea at hsr.it
Wed Jan 31 12:24:43 CET 2007

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.




Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)

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