[gmx-users] Re: gmx-users Digest, Vol 73, Issue 77 (was: gromacs doubt)

Justin A. Lemkul jalemkul at vt.edu
Fri May 14 15:22:52 CEST 2010

manjula kasinathan wrote:
> hi
>      i gave energy minimization for 3000 steps but it runs only 1906 
> steps. these are the files (em.trr, em.edr, em.log) i got after energy 
> minimization. my energy values are
> P.E = -2.6755090e+06
> Maximum force = 9.6265039e+02 an atom 5483
> Norm of force = 1.263261.9e+01

That looks fine.

>          while doing position restrain with these files i got error like
> WARNING 1 [file pr.mdp, line unknown]:
>   Unknown or double left-hand 'warnings' in parameter file
> NOTE 1 [file top.top, line 41]:
>   System has non-zero total charge: -3.400000e+01

Well here's a big problem.  Your system has a net -34 charge!  Life does not 
exist at net charge.  Maybe you should consult some basic tutorial material. 
The use of genion is explained in all of them...

> by using -maxwarn option i ignored the warnings and gone for mdrun it 
> gives error like this

Ignoring warnings is never a good idea.  You have some setting "warnings" in the 
.mdp file that does not exist, so using -maxwarn here is not a major issue, but 
in general, I would recommend never using -maxwarn unless you absolutely know 
why you're ignoring a warning.  Simply trying to plow ahead with fingers crossed 
is a great way to encounter failure.


> hi justin u told me to check the output configuration. i didn't get this 
> line could u tell me which output i have to check.
> i loaded the em.gro file in vmd there is no changes in structure.

Well, certainly energy minimization made some changes if it ran for 1906 steps. 
  Your EM results look fine, I was simply advising you to look for any clashes 
in your structure that perhaps EM did not resolve.


> looking forward for a reply. thanks in advance.
> cheers,
> Manju.


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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