[gmx-users] Error in NVT equilibration

[Vytautas Rakeviius]

Can you explain more to us when it is not appropriate to constrain all bonds during nvt equilibration?
   On Monday, September 17, 2018, 3:06:56 PM GMT+3, Justin Lemkul <jalemkul at vt.edu> wrote:  
 
 

On 9/17/18 8:04 AM, Vytautas Rakeviius wrote:
>  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.

That depends on the force field convention. It is not universally 
appropriate to constrain all bonds (and certainly should not be the 
"solution" to just "make the warning go away"), and the warning from 
grompp may not actually be the source of any problem.

-Justin

>      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,
>
>
> C.

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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