[gmx-users] Restraining one water molecule - settles vs constraints
jalemkul at vt.edu
Thu Oct 26 17:19:47 CEST 2017
On 10/26/17 10:13 AM, Hermann, Johannes wrote:
> 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.
The approach you outlined should work fine. The LINCS warning just
indicates that whatever else you're trying to do is unstable.
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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