杜波 wrote:
dear teacher,
when i do remd in the npt ensemble.
REMD: NPT -replex 4000
dt= 0.0001
step 172000, will finish Sat Dec 31 18:44:12 2011
-------------------------------------------------------
Program mdrun_mpi_4.5.5, VERSION 4.5.5
Source code file: nsgrid.c, line: 549
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
how could i do except using the small dt ?
Your system is not stable, as is often the case with NPT REMD at high
temperature.
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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