Mark, I am quite sure that a difference in the overall simulation time
between two replicas is not going to introduce any bias. Still, you
bring up a good point. If the energy distribution (or even worse, its
average) at a given temperature is affected by the timestep, then this
would be a bad idea. Given the difficulties in converging ST A-values
or (even harder) SREM PDFs, I'm not sure if the answer to this is
known, but I would bet that the timestep is going to influence this
now that you point it out.
Chris.
-- original message --
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.
Mark
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.
--
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