杜波 wrote:
Dear teacher,
when i do remd in the npt ensemble.
it will be bomb when it run a little time .
and the dt is 0.00144,(in my opinion ,it is small enough , in this
condition , the simlution time is about one month )
how could i do except using a small dt.
Please consult:
http://www.gromacs.org/Documentation/Errors#Pressure_scaling_more_than_1.25
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
Without seeing your .mdp file, there's little more to be said. Please also
search the list archive; such issues have been asked and solved hundreds of
times over and there is certainly some useful information already available.
Also note that high-temperature replicates in REMD may be unstable in an NPT
ensemble, largely because the algorithms break down.
-Justin
thanks!!
step 112000, will finish Sun Dec 11 03:59:40 2011
Step 112002 Warning: pressure scaling more than 1%, mu: 48937.5 48937.5
48937.5
-------------------------------------------------------
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.
Variable ci has value 1792617862. It should have been within [ 0 ..
330578952 ]
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
regards,
Bo Du
Department of Polymer Science and Engineering,
School of Chemical Engineering and technology,
Tianjin University, Weijin Road 92, Nankai District 300072,
Tianjin City P. R. China
Tel/Fax: +86-22-27404303
E-mail: 2008d...@gmail.com <mailto:2008d...@gmail.com>
--
========================================
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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