I would look for an error in the input files first.
However, I have a suspicion that this artifact is most likely from a
thermostat problem than LINCS. LINCS may be the object that is
throwing the exception, but in a recent paper by Rosta et.al., it was
shown that weak-coupling thermostats (such as the Berendsen
thermostat) that produce noncanonical ensembles (narrowed fluctuation
amplitude) undergo significant configuration-space distortion under
REMD simulations.
This causes an artificial bias towards exchange of replicas at the
high and low end of the temperature scale. In other words, at some
point during REMD, LINCS ends up having to deal with a superheated
replica showing up at the colder energy levels, forcing it to cope
with extremely high differences in velocity.
Switching to a stronger coupling thermostat may be required in these cases.
<J. Chem. Theory Comput., 2009, 5 (5), pp 1393?1399>
~jared
Quoting [email protected]:
Justin is probably correct, your system is unstable. However, let me
mention another possibility. As the temperature increases, the
largest stable timestep decreases in length. Is it possible that
over some temperature (>1000K?) a 2 fs timestep is no longer viable?
In this case, even a well minimized system with a large number for
lincs_iter is still going to give you incorrect sampling and
possibly crash. You'd need to reduce you highest temperature or
reduce your timestep.
I don't know if the gromacs REMD algorithm allows you to use a
smaller timestep at higher temperatures, but it's something to look
into.
Chris.
-- original message --
For Replica exchange, is there any advantage of in using SHAKE over
LINCS(other than the stepsize)?
I am running an REM simulation and the simulation stops after running for
variable number of steps (100000, 10000000 etc.) because some bond moves
more than 30 degrees and LINCS gives a warning.
Pooja
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