[gmx-users] Restraining one water molecule - settles vs constraints
J.Hermann at lrz.tu-muenchen.de
Thu Oct 26 16:13:09 CEST 2017
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!
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.
*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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