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

[David van der Spoel]

Leonardo Sepulveda Durán wrote:
> 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..

could be, but that's impossible to debug. check the released 3.3 first 
please.
> 
> Leonardo
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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