On 11/20/12 12:17 PM, Ali Alizadeh wrote:
Dear Justin
Thank you for your reply,
1- In the first plot, unit of y axis is kj/mol, and you said above i
should use -nmol, i confused, Why is the unit of y axis kj/mol
without using -nmol?
Because that's the energy unit Gromacs always uses. The
energy given is kJ per
mole of equivalent systems. In the second plot shown above,
the magnitude of
the energy suggests kJ per mole of individual molecules.
I understood,
2- I want do EM so that energy of my system reaches to considered
value, but i never reach it exactly, what's wrong?
You set an EM tolerance of 10 kJ/(mol-nm), which is a force,
and mdrun achieved
that. You can't ask an EM algorithm to produce the same
result as a long-time
MD run, as is shown above.
-Justin
That's right, I knew it but in your opinion, How can i get same
result, What's the value of emtol for my system?
If you want to reproduce the results of an MD trajectory, you need to be doing
MD, not EM.
-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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