On 24/11/2011 6:31 PM, 杜波 wrote:
dear teacher,
when i do remd in the npt ensemble.
=========md.mdp===================
; Start time and timestep in ps
tinit = 0
dt = 0.000001
nsteps = 50000000
; For exact run continuation or redoing part of a run
; Temperature coupling
Tcoupl = nose-hoover
; Groups to couple separately
tc_grps = system
; Time constant (ps) and reference temperature (K)
tau_t = 0.3
ref_t = 800
; Pressure coupling
Pcoupl = berendsen
pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 0.5
compressibility = 6.5e-5
ref_p = 1.0
==========error========================
step 999900, will finish Mon Nov 28 00:11:22 2011
step 1000000, will finish Mon Nov 28 00:11:19 2011
Step 1000002 Warning: pressure scaling more than 1%, mu: 333821 333821
333821
Step 1000002 Warning: pressure scaling more than 1%, mu: 455440 455440
455440
-------------------------------------------------------
Program mdrun_mpi_4.5.5, VERSION 4.5.5
Source code file: smalloc.c, line: 214
Fatal error:
Not enough memory. Failed to realloc -5476105916 bytes for grid->nra,
grid->nra=0x38ce0
(called from file nsgrid.c, line 483)
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
===============command=====================
mpirun n8,8,8,11,11,11,11,2 -np $n_thread
/export/software/bin/mdrun_mpi_4.5.5 -multidir ./0/ ./1/ ./2/ ./3/
./4/ ./5/ ./6/ ./7/ ./8/ ./9/ ./10/ ./11/ ./12/ ./13/ ./14/ ./15/
-replex 500000 -nice 0 -s pmma.tpr -o md -c after_md -pd -v >& log1 &
how could i do except use the smaller dt or big/small tau_p ?
Surprisingly, the URL provided in the error message contains a useful
source of information:
http://www.gromacs.org/Documentation/Errors#Pressure_scaling_more_than_1.25
Mark
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