[gmx-users] Energy minimization Error

[Justin A. Lemkul]

francesca vitalini wrote:
> I achieve
> 
> Steepest Descents converged to machine precision in 205 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  = -1.49131940478719e+07
> Maximum force     =  1.09664530279637e+06 on atom 1520    (parto of the 
> protein)
> Norm of force     =  2.28369808518165e+06
> 

The magnitude of the force suggests atomic overlap somewhere.  Start by 
investigating the environment around atom 1520.

> and the system looked with vmd doesn't look as if it was exploding. 
> However, I have warnings about the table extension and I don't know why 
> but gromacs writes pdb files sometime. However I thought that there 

The "step.pdb" files are written when mdrun is about to crash.

> might have been an error in the way I defined the position restraints, 
> in fact in the mdp file I hade define = -DEPOSRE while in the topology I 
> had ifdef DEFINE_WAT, so it might have moved it all without fixing the 
> water. So I tried again and this time I got
> 

The "define" statements are literal, so be careful of typos.  -DEPOSRE will not 
work when the topology calls for -DPOSRES.  So unless you've changed default 
naming for "define" statements, you're not going to get what you expect.

> Steepest Descents converged to machine precision in 72 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  = -2.0135496e+07
> Maximum force     =  2.0486184e+12 on atom 4479
> Norm of force     =  7.2424045e+13
> 

Again, symptomatic of severe atomic overlap.

> but again the same issue with table extent and still the production of 
> pdb files.
> 
> Any explanations?
> 

Investigate the starting configurations near the problematic atoms.

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-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

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