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
minimization.
-Justin
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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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