[gmx-users] explicit hydrogen-bond

Lars Schaefer Lars.Schaefer at mpi-bpc.mpg.de
Wed Jan 31 16:46:30 CET 2007

Hi again Andrea,
I am not too sure what you exactly mean with your answer, but note that 
there is a difference between a (cartesian) position restraint and a 
distance restraint (see manual). I would 1st run with positional 
restraints on all heavies, 2nd run with distance restraints on all 
critical Hbonds, 3rd production simulation. But annealing as you plan to 
do might also be a good idea. Anyway.

Please also note that an Hbond might very well break and re-form during 
a simulation. So if an Hbond breaks, that means nothing. If breaking / 
reforming happens fast (i.e., on a time scale you can simulate) and you 
see both states several times, you can calculate the free energy 
difference between the broken and Hbonded states very easily via counting.


andrea spitaleri wrote:

> Hi Lars,
> thank for your reply. Indeed you are probably right. On this system I 
> cannot perform successfully a posre (see my previous post). The reason 
> is, I think, that the EM cannot yield to a good minimized structure (the 
> x-ray resolution  is 3.2A very high). My doubt is now about the 
> "restraints". You would use them or nor in the posre simulation? The 
> problem is this ASP-ARG HB is very weak (not a standard angle and 
> distance) and edit specbond for taking in account it, in my opinion, it 
> would mean "cheating".
> This reply should also confirm what Tsjerk says about 
> "solution-crystalline structure".
> I will try without restraint doing short MDs starting at 0K -> 300 and 
> the run a MD a 300K. The other hypothesis is to run also a short MD then 
> a PS and then the full MD.
> I will try both. I let you know
> Thanks for now
> Regards
> Andrea
> Lars Schaefer 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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