[gmx-users] Water molecule starting at atom 5113 can not be settled.
jalemkul at vt.edu
Tue Nov 6 20:12:40 CET 2012
On 11/6/12 2:10 PM, Ali Alizadeh wrote:
> 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)
If mdrun fails to converge, then you shouldn't proceed to MD, since the system
is not at a stable minimum. The most common cause of EM failing is bad atomic
clashes, which means you need more careful system preparation or more delicate
>> 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.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users