On 11/6/12 1:37 PM, Ali Alizadeh wrote:
Dear All users
1- I got an error when i wanted to perform EM, my emtol = 100 but it
did not converge
Water molecule starting at atom 5113 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
...
I saw the pdb files and understood what did the happen,
For solving this error, so i want to perform EM with emtol=1000
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?
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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