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.
-Justin
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
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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