[gmx-users] Iron containing structure simulation crash

Justin Lemkul jalemkul at vt.edu
Tue Aug 12 17:46:40 CEST 2014

On 8/12/14, 11:19 AM, Nikolaos Michelarakis wrote:
> 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

An output coordinate file is always produced unless mdrun completely fails and 
seg faults.  That doesn't mean the coordinates are sane.  It's meant to help you 
diagnose in cases like this where you have an absurd force on some atom.

What is atom 2832?  What's around it?  Is there anything obviously clashing with 
it?  Also check the topology for errors.


> .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,
> Nicholas


Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


More information about the gromacs.org_gmx-users mailing list