[gmx-users] Problem with system minimization

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 16 20:44:22 CET 2009

Lum Nforbi wrote:
> Hello all,
> I am minimizing a system of 2000 water molecules again but I have 
> several error messages. Is my timestep too large indeed? The error 
> message also mentions segmentation fault. I have only 6000 atoms in my 
> system but the output shows atom 7783 and 8879. I'm not sure what's 

Then it seems pretty clear that you don't actually have 2000 water molecules. 
The time step, dt, is irrelevant in EM.  The parameters of primary interest are 
emtol and emstep.

> going on. My pdb file is shown below and the output of the minimization 
> is written after the output.
> Please, help me locate the problem.


> t = 4.066 ps: Water molecule starting at atom 1993 can not be settled.
> Check for bad contacts and/or reduce the timestep.
> Wrote pdb files with previous and current coordinates
> Step= 2034, Dmax= 3.4e-02 nm, Epot=  1.48017e+09 Fmax= 1.08293e+08, 
> atom= 7783

In general:


Your potential energies and maximum forces are astronomically high, suggesting 
unresolvable atomic overlap.  Consider the method you used to construct the 
system, and perhaps that something went very wrong.  Without additional details, 
there's not much else anyone can likely provide that indicates the problem.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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