[gmx-users] constraints

Nicola Staffolani nicola.staffolani at gmail.com
Mon May 12 12:14:11 CEST 2014

Hi everybody,
I am running a simulation of a protein bonded on a metallic structure. In
the mdp files of the MD run I have set

constraints = none

while during the equilibration I had set

constraints = all-bond

in order to reach the MD step with the structure of my protein still in

Well, then I get the following message:

WARNING 1 [file speptide.top, line 11134]:
  The bond in molecule-type Protein_chain_B between atoms 1 N and 2 H1 has
  an estimated oscillational period of 1.0e-02 ps, which is less than 5
  times the time step of 2.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.

​But this is very strange because the bond between the aforementioned atoms
is just copied from the Table of the GROMOS Manual and User Guide.
If then I set ​

​constraints = h-bonds

then mdrun is running​, but I think it should run also with no constraints.
Am I right? Any clue of what is going on? I have also noted that line 11134
of speptide.top is jut the following (bold case) one, i.e. the last one of
the file:

​[ molecules ]
; Compound        #mols
Protein_chain_B     1
SOL             14041
*NA                  1​*

​Thank you very much in advance,


"New ideas, fragile as spring flowers, easily bruised by the tread of the
multitude, may yet be cherished by the solitary wanderer.", Fred Hoyle, *The
Black Cloud*.

"Everybody knows that something can't be done until somebody turns up who
doesn't know that it can't be done and he does it.", Albert Einstein

Sometime ago I met a fellow who was wearing an abnormally long tie - I
mean, it was abnormally long because of how the knot had been made, not
because the tie was an abnormally long one, and so I asked him why such an
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his grandfather!!

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