[gmx-users] EM problem with OPLS and TIP4P

[vechism at netscape.net]

 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 = 100000
 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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