Hi, I'm new to gromacs and I can't figure out what I'm doing wrong with
parallel runs. I'm running gromacs 3.3.2 on a 215 residue protein: 1rz4.pdb.
The 2 missing residues were added with modloop followed by energy minimization.
The protein was put in a dodecahedron box and solvated with a layer of water at
least 1.2 nm from the protein and 14 Na+ ions were added to bring the total
charge of the system to zero. Energy minimization was done to remove close
contacts.
When I run on a single processor my MD runs seem fine (heatup position
restrained MD, constant temperature position restrained MD, and now the
production MD run is almost 86% complete). But when I run on a cluster some I
get strange fatal errors, maybe tripped by boolean checks during writing of
energy info to file. During position restrained MD I got:fatal error in
function do_enx (line 343 of enxio.c) during the call:gmx_fatal(FARGS,"could
not write energies")The fatal error happened after printing Coulomb1-4 energy
in the log file, the next line of headings was NOT printed.
During production run of MD I got:Source code file: stat.c, line: 283Fatal
error: XTC error
happening after writing these lines in the log:
Step Time Lambda 257600 515.20001
0.00000
These errors do not appear when I run equilibriation and production MD on a
single processor on my own machine, but I’d like to take advantage of the
cluster to do runs faster and free up my own machine.
Here’s my .mdp file for the production run:integrator = mdnsteps =
500000dt = 0.002nstlist = 10rlist = 1.2coulombtype
= pmercoulomb = 1.2vdw-type = cut-offrvdw = 1.2tcoupl
= Berendsentc-grps = protein non-proteintau-t = 0.1
0.1ref-t = 300 300pcoupl = Berendsentau-p =
1.0compressibility = 5e-5ref-p = 1.0nstxout = 1000nstvout
= 1000nstxtcout = 100nstenergy = 100constraints = allbonds;
Generate velocites is on at 300 K.gen_vel = yes
The same .top, .gro, .mdp and .tpr files are used on both single processor and
parallel runs, with the GROMOS96 53a6 force field. Any help you can offer is
much appreciated!
Thanks,Patricia Francis-Lyon
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