[gmx-users] LINCS vs SHAKE

[thompsjj at purdue.edu]

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 chris.neale at utoronto.ca:

> 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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