On 8/2/12 9:57 AM, Christian Blouin wrote:
My simulation aborts rather quickly because it accumulates too many
LINCS warning. I checked the various plots and everything seems to be
stable (temperature, pressure, total energy, etc.). The stderr gives
me warnings looking like this:
Step 2304252, time 4608.5 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.043352, max 0.606635 (between atoms 150 and 151)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
150 152 90.0 0.0985 0.1490 0.1000
150 151 90.0 0.1314 0.1607 0.1000
The problem I see is that atom 150 and 151 do not even have a bond
between them (they are the two hydrogens of one water molecule). I
also get similar warning between 150 and 152, which are not even on
the same water molecule. I have extensively equilibrated the system as
I thought that it was the problem originally.
If that's true, then something is more fundamentally wrong. The constraint
length of 0.1 nm indicates an O-H bond, which makes sense if atom 150 is
actually an O, making 151 and 152 H atoms. H-H constraints are possible if
using the SETTLE algorithm for rigid water, but in this case something seems
inconsistent.
Anyone here has an intuition as to why this may happen?
LINCS warnings always indicate generic instability in the system. The only real
advice is here:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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