[gmx-users] Restraining one water molecule - settles vs constraints

[Justin Lemkul]

On 10/26/17 10:13 AM, Hermann, Johannes wrote:
> Hi Justin,
>
> yes everything is clear in the manual.
>
> What I now get are lincs warnings for the OW-HW1 and OW-HW2 bond:
>
> (exemplary for the OW-HW1 bond):
>
> LINCS WARNING in simulation 1
> relative constraint deviation after LINCS:
> rms 0.317574, max 0.547778 (between atoms 1 and 2)
> bonds that rotated more than 30 degrees:
>
> Corresponding lincs parameters in the mdp file:
>
> ; options for bonds
> constraints              = h-bonds
> constraint-algorithm     = lincs
> lincs-order              = 4
>
> Do I have to change anything else in the itp file for my "special" 
> water (which I generated from tip3p.itp)? Currently I only changed the 
> [ settles ] - section into the [ constraints ] section.
>

The approach you outlined should work fine. The LINCS warning just 
indicates that whatever else you're trying to do is unstable.

-Justin

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

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