[gmx-users] LINCS vs SHAKE

Mark Abraham Mark.Abraham at anu.edu.au
Sun Oct 31 02:12:35 CET 2010

On 31/10/2010 10:04 AM, chris.neale at utoronto.ca wrote:
> 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.
It doesn't. Off the cuff, I can't say whether it's sound to simulate at 
a smaller timestep at higher temperature and exchange with a simulation 
that has done the same number of larger timesteps.

> 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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