[gmx-users] Error in NVT equilibration

Vytautas Rakeviius vytautas1987 at yahoo.com
Mon Sep 17 14:04:44 CEST 2018

 I think your attachment to email was lost during re-transfer and it would be nice to see that, but I think what you need is:constraints	            = all-bondsIn that mdp file.

    On Friday, September 14, 2018, 4:07:43 PM GMT+3, Gonzalez Fernandez, Cristina <cristina.gonzalezfdez at unican.es> wrote:  
 Dear Gromacs users,

I am trying to perform a nvt equilibration, but when I generate the .tpr file I get a warning indicating that a bond is oscillating too fast:

The bond in molecule-type MOL_1 between atoms 38 C21 and 39 O22 has an estimated oscillational period of 2.4e-02 ps, which is less than 5 times the time step of 1.5e-02. Maybe you forgot to change the constraints mdp option.

I have ignored it with the -maxwarn option and I obtain the .tpr file. However, when I run the simulation I obtain this error?

Too many LINCS warnings (1630)

Are the error and the warning related? How could I solve the Lincs error and the warning?

I attach the .mdp file.

Thank you in advance,

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