[gmx-users] LINCS vs SHAKE

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sun Oct 31 01:04:34 CEST 2010

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.


-- 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.


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