[gmx-users] Iron containing structure simulation crash

Nikolaos Michelarakis nm884 at york.ac.uk
Tue Aug 12 17:19:41 CEST 2014

Hello again,

I finally managed to introduce the iron into my structure and generate a
topology. However, when i first run the initial energy minimization, either
in vacuum or with solvent, i get the following message:

It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often
notneeded for preparing to run molecular dynamics.
writing lowest energy coordinates.

Steepest Descents converged to machine precision in 36 steps,
but did not reach the requested Fmax < 500.
Potential Energy  = -4.2946888e+05
Maximum force     =  6.7161971e+08 on atom 2832
Norm of force     =  1.7847602e+07

however, a .gro file is produced. When I try to run the next step with this
.gro file I get a bunch of LINCS warnings  and after a few steps the
simulation crashes with this message:

/opt/gridengine/default/spool/compute-0-5/job_scripts/11107: line 15:  5738
Segmentation fault      (core dumped) mdrun -v -nt 12 -deffnm nvt-pr

I also get a bunch of .pdb files named accordingly to each step.

Could anyone explain to me what is going wrong? I can provide links to all
files if required.

Thanks again,


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