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

[Hermann, Johannes]

Hi Justin,

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

Thanks, Justin!

All the best

Johannes


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 
>> 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
>>
>

-- 
______________________________________
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
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Email: j.hermann at lrz.tum.de
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