[gmx-users] Water molecule starting at atom 5113 can not be settled.

Ali Alizadeh ali.alizadehmojarad at gmail.com
Tue Nov 6 20:10:54 CET 2012

Dear Justin

    >What did you do to fix the problem?

> it converged,  in next step i got em.gro as a input file and perform
> another EM with emtol=900
> It converged , and i continued to emtol=100

           >  Did it work the second time?

Yes, But i got a lot of errors in my md run,

in your opinion, how can i solve this error?

I reduced my dt,

My system is biphasic(water and methane and propane and methane in 300
bar and 240 k, ff is gromos45a3)

> Is my method true?  I do not know my energy profile(i got by this
> method)  is correct,
> 2- Does this parameter affect on my md production? (when i use
> emtol=1000 or emtol=100)

      > The tolerance setting the desired value of Fmax.  If the EM
algorithm reaches a
       >force below the tolerance, it finishes.  Without knowing what
your system is or
        >    what you intend to do, it's impossible to state what
level of emtol is sufficient.



Ali Alizadeh

More information about the gromacs.org_gmx-users mailing list