[gmx-users] energy minimization of a box containing two Na+ ions and water does not converge

[Justin A. Lemkul]

Ozge Engin wrote:
> Hi all,
> 
> I have been trying to calculate the PMF of two NA+ ions in explicit bulk 
> water. First, I tried to calculate the mean force between the two ions 
> at a distance of 0.48 nm, which is big enough than the diameter of the 
> ions. I first energy minimized the system with the script below, but it 
> did not converge. After that, I removed one of the ions, and tried 
> again, it did not work again.
> 
> I am using ffG43a1 ff, and checked whether I used the correct naming for 
> the ion: Everything seems to be OK.
> 

Irrelevant.  If naming were an issue, grompp would have failed with a fatal error.

> I could not attach the initial coordinate file due to the limited size. 
> If you want I can also sent it to you as well.
> 
> *Script: *
> title               =  Minimization
> cpp                 =  /usr/bin/cpp
> define              =  -DFLEX_SPC
> constraints         =  none
> integrator          =  steep
> dt                  =  0.002    ; ps !
> nsteps              =  30000
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.0
> vdwtype             =  cut-off
> coulombtype         =  PME
> rcoulomb            =  1.0
> rvdw                =  1.4
> fourierspacing      =  0.12
> pme_order           = 4
> ewald_rtol          = 1e-5
> optimize_fft        = yes
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  100.0
> emstep              =  0.01
> 
> 
> *Output*:
> 
> Steepest Descents converged to machine precision in 36 steps,
> but did not reach the requested Fmax < 100.
> Potential Energy  = -1.0409969e+05
> Maximum force     =  9.6685031e+04 on atom 294
> Norm of force     =  1.4924829e+03
> 
> What may be the problem?

Not a clue.  What is atom 294?  Look at the output - what are the other nearby 
atoms that could be causing the excessive force?

-Justin

> 
> Best Regards
> 
> -- 
> Ozge Engin
> ★☆
> 

-- 
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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

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