[gmx-users] Error in NVT equilibration

[Vytautas Rakeviius]

 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?


    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.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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