[gmx-users] Can not run energy minimization for the protein-lipid system.

Justin Lemkul jalemkul at vt.edu
Sun Aug 9 19:05:51 CEST 2015

On 8/9/15 12:55 PM, Vy Phan wrote:
> Dear Gromacs Users
> I run membrane protein with DOPC lipip. Without protein, the
> lipid-ions-water system can run energy minimization. But when I insert
> protein in the center of that system (I removed the overlapping molecules),
> but this system can not run. I always got this message. Actually, I do not
> know where is the error come from.
> Could someone help me?
> Polak-Ribiere Conjugate Gradients:
>     Tolerance (Fmax)   =  1.00000e+01
>     Number of steps    =         5000
>     F-max             =          inf on atom 89

Infinite force = something catastrophically wrong with the coordinates or 
topology.  Inspect atom 89 and its neighbors to see if there's some obvious 
atomic overlap, which is the most likely cause.


>     F-Norm            =          inf
> Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 10 (which may not be possible for your system).
> 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 not
> needed for preparing to run molecular dynamics.
> WARNING: there may be something wrong with energy file em.edr
> Found: step=-1, nre=33, nblock=0, time=-1.
> Trying to skip frame expect a crash though
> writing lowest energy coordinates.
> Back Off! I just backed up em.gro to ./#em.gro.1#
> Polak-Ribiere Conjugate Gradients converged to machine precision in -1
> steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  =  3.8252541e+26
> Maximum force     =            inf on atom 89
> Norm of force     =            inf
> Thank in advance
> Phan Vy


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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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