Dear Gromacs users,
I am trying to run a MD simulation of a protein using OPLS and TIP4P in the same way as I already did before using GROMOS and SPC water but when I run the mdrun for the Energy Minimization I get the error described below.
These errors occur during the EM (the mdp file is enclosed):
(a) using only one processor:
Step 20, Epot=-1.117652e+07, Fnorm=2.168e+03, Fmax=6.133e+03 (atom 12802)
Step 21, Epot=-1.188519e+07, Fnorm=2.613e+03, Fmax=1.336e+04 (atom 3990)
Step 22, Epot=-1.193758e+07, Fnorm=2.724e+03, Fmax=1.581e+04 (atom 3990)
Step 23, Epot=-1.492766e+07, Fnorm=2.250e+04, Fmax=2.177e+06 (atom 3990)
Step 24, Epot=-1.276652e+22, Fnorm= inf, Fmax= inf (atom 86)
In this case, the program do not display any error messages, just stay running but do not
return anything else.
(b) using two processors:
Step 20, Epot=-1.117643e+07, Fnorm=2.168e+03, Fmax=6.133e+03 (atom 1)
Step 21, Epot=-1.188507e+07, Fnorm=2.613e+03, Fmax=1.336e+04 (atom 3990)
Step 22, Epot=-1.193749e+07, Fnorm=2.724e+03, Fmax=1.581e+04 (atom 3990)
Step 23, Epot=-1.492768e+07, Fnorm=2.250e+04, Fmax=2.177e+06 (atom 3990)
Step 24, Epot= nan, Fnorm= nan, Fmax= inf (atom 36)
Fatal error: ci = -2147483648 should be in 0 .. 511 [FILE nsgrid.c, LINE 218]
Fatal error: ci = -2147483648 should be in 0 .. 511 [FILE nsgrid.c, LINE 218]
-
One of the processes started by mpirun has exited with a nonzero exit
code. This typically indicates that the process finished in error.
If your process did not finish in error, be sure to include a "return
0" or "exit(0)" in your C code before exiting the application.
PID 7295 failed on node n0 (127.0.0.1) with exit status 32767.
-
(c) using 1 processor and a bigger simulation box:
Step 20, Epot=-1.632885e+07, Fnorm=2.296e+03, Fmax=6.372e+03 (atom 32295)
Step 21, Epot=-1.716738e+07, Fnorm=2.151e+03, Fmax=6.880e+03 (atom 10791)
Step 22, Epot=-1.966934e+07, Fnorm=7.181e+03, Fmax=8.281e+04 (atom 22371)
Step 23, Epot=-1.973746e+07, Fnorm=7.382e+03, Fmax=1.002e+05 (atom 22371)
Step 24, Epot= nan, Fnorm= nan, Fmax=2.685e+06 (atom 4546)
Fatal error: ci = -2147483648 should be in 0 .. 728 [FILE nsgrid.c, LINE 218]
-
A piece of my mdp file:
;
cpp = /lib/cpp
define = -DFLEXIBLE
constraints = none
integrator = cg
;integrator = steep
nsteps = 10
unconstrained_start = yes
nstxout = 100
nstvout = 100
nstfout = 100
nstlog = 100
nstenergy = 100
;
; ENERGY MINIMIZATION OPTIONS
;
; Force tolerance and initial step-size
emtol = 100
emstep = 0.0001
;
; Frequency of steepest descents steps when doing Conjugated Gradient
nstcgsteep = 10
The atoms: 86 in (a), 36 in (b) and 4546 in (c) are hydrogen atoms.
I have read the mailing list and whereas I found some similar errors I haven't found
the answer yet.
Could someone help me with some clues?
Thanks in advance,
Sergio
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