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<div>Dear Gromacs users,<br>
<br>
<br>
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.<br>
<br>
These errors occur during the EM (the mdp file is enclosed):<br>
<br>
(a) using only one processor:<br>
<br>
Step 20, Epot=-1.117652e+07, Fnorm=2.168e+03, Fmax=6.133e+03 (atom 12802)<br>
Step 21, Epot=-1.188519e+07, Fnorm=2.613e+03, Fmax=1.336e+04 (atom 3990)<br>
Step 22, Epot=-1.193758e+07, Fnorm=2.724e+03, Fmax=1.581e+04 (atom 3990)<br>
Step 23, Epot=-1.492766e+07, Fnorm=2.250e+04, Fmax=2.177e+06 (atom 3990)<br>
Step 24, Epot=-1.276652e+22, Fnorm= inf, Fmax= inf (atom 86)<br>
<br>
In this case, the program do not display any error messages, just stay running but do not <br>
return anything else.<br>
<br>
<br>
(b) using two processors:<br>
<br>
Step 20, Epot=-1.117643e+07, Fnorm=2.168e+03, Fmax=6.133e+03 (atom 1)<br>
Step 21, Epot=-1.188507e+07, Fnorm=2.613e+03, Fmax=1.336e+04 (atom 3990)<br>
Step 22, Epot=-1.193749e+07, Fnorm=2.724e+03, Fmax=1.581e+04 (atom 3990)<br>
Step 23, Epot=-1.492768e+07, Fnorm=2.250e+04, Fmax=2.177e+06 (atom 3990)<br>
Step 24, Epot= nan, Fnorm= nan, Fmax= inf (atom 36)<br>
Fatal error: ci = -2147483648 should be in 0 .. 511 [FILE nsgrid.c, LINE 218]<br>
Fatal error: ci = -2147483648 should be in 0 .. 511 [FILE nsgrid.c, LINE 218]<br>
-----------------------------------------------------------------------------<br>
One of the processes started by mpirun has exited with a nonzero exit<br>
code. This typically indicates that the process finished in error.<br>
If your process did not finish in error, be sure to include a "return<br>
0" or "exit(0)" in your C code before exiting the application.<br>
<br>
PID 7295 failed on node n0 (127.0.0.1) with exit status 32767.<br>
-----------------------------------------------------------------------------<br>
<br>
<br>
(c) using 1 processor and a bigger simulation box:<br>
<br>
Step 20, Epot=-1.632885e+07, Fnorm=2.296e+03, Fmax=6.372e+03 (atom 32295)<br>
Step 21, Epot=-1.716738e+07, Fnorm=2.151e+03, Fmax=6.880e+03 (atom 10791)<br>
Step 22, Epot=-1.966934e+07, Fnorm=7.181e+03, Fmax=8.281e+04 (atom 22371)<br>
Step 23, Epot=-1.973746e+07, Fnorm=7.382e+03, Fmax=1.002e+05 (atom 22371)<br>
Step 24, Epot= nan, Fnorm= nan, Fmax=2.685e+06 (atom 4546)<br>
Fatal error: ci = -2147483648 should be in 0 .. 728 [FILE nsgrid.c, LINE 218]<br>
<br>
-------------------------------------------------------------------------------------<br>
<br>
<br>
A piece of my mdp file:<br>
********************************************************************<br>
;<br>
cpp = /lib/cpp<br>
define = -DFLEXIBLE<br>
constraints = none<br>
integrator = cg<br>
;integrator = steep<br>
nsteps = 100000<br>
unconstrained_start = yes<br>
nstxout = 100<br>
nstvout = 100<br>
nstfout = 100<br>
nstlog = 100<br>
nstenergy = 100<br>
;<br>
; ENERGY MINIMIZATION OPTIONS<br>
;<br>
; Force tolerance and initial step-size<br>
emtol = 100<br>
emstep = 0.0001<br>
;<br>
; Frequency of steepest descents steps when doing Conjugated Gradient<br>
nstcgsteep = 10<br>
************************************************************************<br>
<br>
The atoms: 86 in (a), 36 in (b) and 4546 in (c) are hydrogen atoms.<br>
<br>
I have read the mailing list and whereas I found some similar errors I haven't found<br>
the answer yet.<br>
<br>
Could someone help me with some clues?<br>
<br>
Thanks in advance,<br>
<br>
<br>
Sergio<br>
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