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dubo

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[求助] remd :Step 1000002 Warning: pressure scaling more than 1%

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 ?

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1樓 2011-11-26 16:39:49

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hcf春妮

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樓主您好，今日我在用Gromacs做REMD，看了官網(wǎng)還是不太清楚做REMD的步驟，目前知道的內(nèi)容是先選取溫度然后做預(yù)平衡做MD，接著再做REMD，可是具體的步驟不太了解，如果樓主能夠看到，希望得到您的回復(fù)

贊一下

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2樓2017-04-25 16:29:20

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