[gmx-users] Editing of the existing system

Justin A. Lemkul jalemkul at vt.edu
Sun Apr 1 19:37:32 CEST 2012

James Starlight wrote:
> Justin,
> Sorry again for the delay.
> I've finished minimise my system with the CG algorithm in double 
> precision ( after steep minimisation )
> but the output was
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 0.1
> Than I've tried to equilibrate this system with the NVT conditions and 
> obtain old error about collapse of my system :)
>  I've found logs of both minimisation ( the step minimisation log was 
> very big I've coppied only end part of this output data )  and attach it 
> to this topic.

Both of these log files indicate that EM was likely fine.  For future reference, 
the following sections were all I was asking for all along:

 From CG:
Potential Energy  = -5.96597537065782e+05
Maximum force     =  1.42815783701700e+02 on atom 1388
Norm of force     =  1.58963638409829e+00

 From steep:
Potential Energy  = -5.7233788e+05
Maximum force     =  7.0209003e+02 on atom 1388
Norm of force     =  1.1310696e+01

CG gives you the better minimization, overall, as expected.  Atom 1388 bears the 
maximum force, but it is not of problematic magnitude.

> Also I've run minimisation in vacuum as you've told me but this results 
> would be aviable tomorrow.

It's probably not necessary, after all.  I was guessing at that point based on 
incomplete information.

> Could you tell me whats exactly wrong with that system and is there 
> possible ways to fix the problem?

As I've said before, the only strange thing you seem to be doing is with your 
comm-grps.  Change this setting to "System" and see if it runs.  Otherwise, I 
can find no reason for the immediate instability.  If it still crashes, perhaps 
decrease the time step for the initial equilibration.



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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