[gmx-users] Restraining one water molecule - settles vs constraints
jalemkul at vt.edu
Thu Oct 26 15:00:44 CEST 2017
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
>>> /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
> 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
> [ 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
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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