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

Dawid das addiw7 at googlemail.com
Sat May 6 15:36:02 CEST 2017

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
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 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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