[gmx-users] Editing of the existing system

[Justin A. Lemkul]

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

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================