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

[Justin Lemkul]

On 10/26/17 8:58 AM, Hermann, Johannes wrote:
> Dear Gromacs Users, dear Justin,
>
> I am using the tip3p water model and I want to restrain one single 
> water molecule. I found Justins reply in the mailing list a few years 
> ago:
>
>>> /If you want to restrain a single water molecule, it needs to be 
>>> defined as />>/its own [moleculetype] or as a part of the protein 
>>> [moleculetype]. 
> Breaking />>/apart a continuous block of water causes problems with 
> the SETTLE />>/algorithm, so you will need to manually specify three 
> constraints (OW-HW1, />>/OW-HW2, and HW1-HW2) for this water molecule, 
> while the remaining bath of />>/solvent would be handled by SETTLE. 
> />>//>>/-Justin /
>
> I looked up in the manual how the constraints-section is formated, but 
> I have no glue about the funct type. Perhaps funct 1? For the lengths 
> of OW-HW1 and OW-HW2 I would assume that I take the bond-lengths 
> specified in tip3p.itp, but I have no idea about the HW1-HW2 length.
>

You can find it in the SETTLE information in tip3p.itp:

[ settles ]
; i j   funct   length
1   1   0.09572 0.15139

-Justin

> [ constraints ]
> ; i   j funct   length
> 1     2  1  0.09572
> 1     3  1  0.09572
> 2     3  1  ??
>
> Can anyone help me?
>
> Thank you very much!
>
> All the best
> Johannes
>

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

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