[gmx-users] Problem with dynamics using ENDADS and CVS GMX version

[Leonardo Sepulveda Durán]

Hello!

I am trying to make simulations with ENCADS. I use the following protocol:

SETUP
1.	pdb2gmx -f  input.pdb  | option 10 (encads)
2.	editconf -bt tric -f conf.gro-o conf.gro -c -princ -d 0.8
3.	genbox -cp  conf.gro -cs spc216.gro -o conf.gro -p topol.top

MIN
4.	grompp -f EMCG.mdp -c  conf.gro -p topol.top -o min.tpr -np 2
5.       nohup mpirun -np 2 mdrun_mpi -s min.tpr -o min.trr -c min.gro  &

PR
6.       grompp -f PR.mdp -c  min.gro  -p topol.top -o pr.tpr -np 2
7.       nohup mpirun -np 2 mdrun_mpi  -s pr.tpr -o pr.trr -c din.gro &

DIN
8.       grompp -f SA.mdp -c  pr.gro  -p topol.top -o din.tpr
9.       nohup mpirun -np 2 mdrun_mpi  -s din.tpr -o din.trr -c din.gro &

All works fine untill DIN. This is SA .inp:

title          		          = Simulated annealing
cpp            	           	= /lib/cpp  	
constraints    		= none 	
integrator     		= md
;	Molecualr Dynamics
dt             		          = 0.001 	; ps !
nsteps         		= 1050000  	; 100 ps
comm_mode                = linear
nstcomm                       = 1
nstxout        		= 1000 		
nstvout        		= 1000 		
nstfout        		= 0 		
nstenergy     		= 1000
;	Nonbond
nstlist        		          = 5 		
ns_type        		= grid
rlist          		          = 1.0
coulombtype    		= encadshift
vdwtype 		          = encadshift
rcoulomb       		= 0.8 		
rvdw           		          = 0.8 		
; 	Temp coupling
Tcoupl         		= berendsen
tau_t          		          = 0.1     0.1
tc-grps        		= Protein SOL
ref_t          		          = 300     300 	
;	Annealing
annealing      		= single single
annealing_npoints	= 2      2
annealing_time 		= 0 50   0 50
annealing_temp          = 0 300  0 300

The simulation is Ok untill step 37200, then it stops without any kind
of warning or  error. This is the final of the output file (nohup.out)

Reading file din.tpr, VERSION 3.3 (single precision)
starting mdrun 'in water'
1050000 steps,   1050.0 ps.

-----------------------------------------------------------------------------
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 2143 failed on node n0 (192.168.1.11) due to signal 11.
-----------------------------------------------------------------------------

I really dont Know what is happening. Could someone help me?

The gromacs version I used was the CVS version downloaded one month
ago. Is maybe a Bug? or maybe the input file have some trouble, but is
not evident for me..

Leonardo