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