[gmx-users] constraints

[Nicola Staffolani]

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
order.

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 2.5.2.1 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,

Nicola​

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