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

[Hermann, Johannes]

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.

Thanks in advance!

Johannes

On 26.10.2017 15:25, Justin Lemkul wrote:
>
>
> On 10/26/17 9:19 AM, Hermann, Johannes wrote:
>> 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
>>
>
> Yes. For reference, the contents of SETTLE are described in full in 
> manual section 5.6, hopefully nothing is misleading there.
>
> -Justin
>

-- 
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*Technische Universität München*
*Johannes Hermann, M.Sc.*
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