Hi Joern,
this problem has definately nothing to do with your mdp file and is in
fact not related to GROMACS.
To know what went wrong, it would help to know more about how you
submitted your job. My guess would be that you killed the shell which
hosted your job or sth like this.
try submitting the job using "nohup" in front of your "mdrun" command,
and don;t forget to use the "&" at the end
Lars
Joern Lenz wrote:
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
------------------------------------------------------------------------
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