nicola.staffolani at gmail.com
Mon May 12 12:14:11 CEST 2014
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 220.127.116.11 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
[ molecules ]
; Compound #mols
Thank you very much in advance,
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