[gmx-users] mdrun on several clusternodes using PME gromacs 3.3.1

[Joern Lenz]

dear users,
i wanted to simulate a DNA in a box of water using PME and run the calculation 
on a cluster with 16 nodes.
i used the following mdp (see at the bottom of this mail)  file and then 
submitted the job to our cluster. unfortunately i always get the following 
output:
50000 steps,    100.0 ps.
Killed by signal 2. 
Killed by signal 2. 
Killed by signal 2. 
Killed by signal 2. 
Killed by signal 2. 
Killed by signal 2. 
Killed by signal 2. 
Killed by signal 2. 
Killed by signal 2. 
Killed by signal 2. 
Killed by signal 2. 
Killed by signal 2. 
Killed by signal 2. 
Killed by signal 2. 
Killed by signal 2. 
mdrun01 finished

has anyone an idea of the reason for this problem. 
many thanks in advance
greetings from hamburg
joern

this is my mdp-file: 
cpp           = /usr/bin/cpp       ; preprocessor
define        = -DPOSRES
constraints   = all-bonds 
integrator    = md            
dt            = 0.002
nsteps        = 50000
nstcomm       = 1
nstvout       = 1000 
nstxout       = 1000               
nstfout       = 0  
nstlog        = 1000          
nstenergy     = 1000
nstlist       = 10             
ns_type       = grid             
coulombtype     = PME          
fourierspacing  = 0.12 
fourier_nx      = 0
fourier_ny      = 0
fourier_nz      = 0
pme_order       = 4
ewald_rtol      = 1e-5
optimize_fft    = yes
rlist         = 0.9        
rcoulomb      = 0.9          
rvdw          = 1.4      
pbc           = xyz            

; ****************************************************
; Berendsen temperature coupling is on
; ****************************************************
tcoupl      =  berendsen      
tau_t        = 0.1    1.0      0.5          0.5         0.5        0.5  
tc_grps    = Sol    NA+    DGUA      DADE    DCYT    DTHY
ref_t         = 100   100     100         100        100       100                   

; ***********************
; Pressure coupling is on 
; ***********************

pcoupl          = berendsen       
tau_p           = 0.5              
compressibility = 4.5e-5  
ref_p           = 1.0
gen_vel       = yes           
gen_temp      = 100.0            
gen_seed      = 173529           
-------------- next part --------------
dear users,
i wanted to simulate a DNA in a box of water using PME and run the calculation on a cluster with 16 nodes.
i used the following mdp (see at the bottom of this mail) file and then submitted the job to our cluster. unfortunately i always get the following output:
50000 steps, 100.0 ps.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
mdrun01 finished
has anyone an idea of the reason for this problem.
many thanks in advance
greetings from hamburg
joern
this is my mdp-file:
cpp = /usr/bin/cpp ; preprocessor
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002
nsteps = 50000
nstcomm = 1
nstvout = 1000
nstxout = 1000
nstfout = 0
nstlog = 1000
nstenergy = 1000
nstlist = 10
ns_type = grid
coulombtype = PME
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
rlist = 0.9
rcoulomb = 0.9
rvdw = 1.4
pbc = xyz
; ****************************************************
; Berendsen temperature coupling is on
; ****************************************************
tcoupl = berendsen
tau_t = 0.1 1.0 0.5 0.5 0.5 0.5
tc_grps = Sol NA+ DGUA DADE DCYT DTHY
ref_t = 100 100 100 100 100 100
; ***********************
; Pressure coupling is on
; ***********************
pcoupl = berendsen
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
gen_vel = yes
gen_temp = 100.0
gen_seed = 173529