[gmx-users] Error in NVT equilibration

[Justin Lemkul]

On 9/17/18 8:37 AM, Vytautas Rakeviius wrote:
>   And what about OPLS-AA/L if I do nvt equilibration of my protein in water with it is it OK to do constraints	            = all-bondsall the time like I am used to do?
>

I would encourage you to examine the primary literature for the force 
field, understand what its conventions are, and apply whatever is 
correct for that force field.

-Justin

>      On Monday, September 17, 2018, 3:18:51 PM GMT+3, Justin Lemkul <jalemkul at vt.edu> wrote:
>   
>   
>
> On 9/17/18 8:12 AM, Vytautas Rakeviius wrote:
>> Can you explain more to us when it is not appropriate to constrain all bonds during nvt equilibration?
> The use of constraints is not tied to the statistical mechanical
> ensemble or the simulation process (equilibration, production, etc).
> Constraints are a convention of force fields. For example, it is stated
> in the primary literature for the GROMOS force fields that all bonds are
> constrained. That is an assumption within the physical model, and proper
> use of that force field dictates that the user should follow that
> convention. For CHARMM, only bonds to H are to be constrained, because
> the bond vibrations are expected to be present. Every intramolecular
> interaction is linked - if you violate the force field convention with
> respect to bonds, then the angle vibrations are inconsistent with the
> parametrization, the dihedrals (which are tied to both bonds and angles)
> are not necessarily employed correctly, etc.
>
> The main point: every element of a force field, from its cutoffs, water
> model, use of constraints, etc. is linked. While there are deviations
> from this "absolute" statement in certain cases, consider this a pretty
> strong rule for doing accurate and reliable simulations. There are not
> as many choices to be made as one might expect.
>
> -Justin
>
>>      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
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