[gmx-users] Restraining one water molecule - settles vs constraints
J.Hermann at lrz.tu-muenchen.de
Thu Oct 26 15:19:25 CEST 2017
thanks for the quick response! Ahhh! I looked into the manual for [
settles ] and "i j funct length" is kind of misleading.
So this should work, right?
[ constraints ]
; i j funct length
1 2 1 0.09572
1 3 1 0.09572
2 3 1 0.15139
All the best
On 26.10.2017 15:00, Justin Lemkul wrote:
> 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
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Tel: +49 8928915730
Fax: +49 8928915714
Email: j.hermann at lrz.tum.de
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