On 31/10/2010 10:04 AM, chris.ne...@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.
Pooja
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
