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

[Lars Schaefer]

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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