[gmx-users] BONDS BREAK DURING MINIMIZATION

[Justin Lemkul]

On 12/3/17 5:07 AM, Vidya R wrote:
> Hi gromacs users,
>
> The bonds of my organic molecule, break while computing rdf.

Bonds cannot break in a molecular mechanics process, by definition.

If you are getting a distorted structure (which your visualization 
software subsequently guesses does not have bonds, which is wrong), that 
likely means your topology is incorrect.

-Justin

> The following sentences appear while first minimization
>
> Step 11, time 0.011 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000002, max 0.000079 (between atoms 20 and 6)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>       31     13   37.2    0.1080   0.1080      0.1080
>       32     14   32.3    0.1080   0.1080      0.1080
>
> Step 12, time 0.012 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000003, max 0.000196 (between atoms 21 and 6)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>       31     13   45.5    0.1080   0.1080      0.1080
>       32     14   38.3    0.1080   0.1080      0.1080
>
> Step 15, time 0.015 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000005, max 0.000318 (between atoms 21 and 6)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>       31     13   30.7    0.1080   0.1080      0.1080
>
> Step 16, time 0.016 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000002, max 0.000043 (between atoms 20 and 6)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>       31     13   38.4    0.1080   0.1080      0.1080
>       32     14   37.0    0.1080   0.1080      0.1080
>
> Step 20, time 0.02 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000003, max 0.000143 (between atoms 21 and 6)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>       31     13   32.5    0.1080   0.1080      0.1080
>
>
> HOw to fix it?
>
> Thanks,
> Vidya.R

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

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