[gmx-users] Heavy atom - hydrogens bond lengths constraints.

[Jochen Hub]

Am 06.05.17 um 15:35 schrieb Dawid das:
> Dear Gromacs Users,
>
> I am a bit anxious about the results I get for my simulation of protein in
> a box of water using CHARMM 27 force field.
> Namely, even though I use following options to constrain bond lengths
> between
> hydrogen atoms and heavy atoms:
>
> constraint_algorithm    = lincs
> constraints                 = h-bonds
> lincs_iter                  = 1
> lincs_order                 = 4
>
> and I do not use
>
> define = -DFLEXIBLE
>
> so if I understand correctly I do simulate rigid water molecules, right?
>
> Anyway, I observe fluctutations of bond lengths between hydrogen atoms and
> heavy atoms
> with amplitude up to 0.020 AA.

Is this possibly due to the limited precision of xtc files? Do you get 
the same when reading the trr file?

>
> Is this what I can expect? Also, I can clearly see that my water molecules
> (TIP3P model) are not stiff.
>
> Best wishes,
> Dawid Grabarek
>

-- 
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Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189
http://cmb.bio.uni-goettingen.de/
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